Welcome to the California Fisheries Blog

The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.

How do we increase salmon runs in 2017?

Over the past few months, I have written posts on the status of specific runs of salmon in rivers throughout the Central Valley.  In this post, I describe the overall status of salmon runs and  recommend general actions to take to increase runs as well as commercial and sport fishery harvests.  The subject is timely given a poor prognosis for the 2017 salmon runs.

It was just a little more than a decade ago at the beginning of the century that there were nearly one million adult salmon ascending the rivers of the Central Valley (Figure 1).  At the same time, there were a million more Central Valley salmon being harvested each year in sport and commercial fisheries along the coast and in the rivers of the Central Valley.  Improvements in salmon management in the decade of the 1990s by the Central Valley Project Improvement Act, CALFED, and other programs had paid off handsomely with strong runs from 1999 to 2005.  New and upgraded hatcheries, combined with the implementation of  trucking hatchery smolts to the Bay, significantly increased both harvest and escapement to spawning rivers.

Figure 1. Central Valley salmon runs from 1975 to 2016 including fall, late fall, winter, and spring runs. Source of data: CDFW GrandTab.

By 2008-2009 escapement had fallen by over 90% to a mere 70,000 spawners of the four major Central Valley runs of salmon.  DFW and the Pacific Fishery Management Council greatly restricted fishery harvest of salmon beginning in 2008.  The winter run, the most threatened of the four runs, fell from 17,296 to 827 spawners in just five years.  Drier years from 2001-2005, poor ocean conditions in 2004-2005, record-high Delta water diversions, and the 2007-2009 drought were contributing factors in these declines.  Impacts to coastal communities and the fishing industries were severe.

Extraordinary recovery measures included closing fisheries and trucking most of the hatchery smolt production to the Bay or Delta.  Federal salmon biological opinions (2009, 2011) limited winter and spring water-project exports from the Delta.  The state and federal governments and others spent hundreds of millions of new dollars on habitat and fish passage improvements in the Valley to improve salmon survival and turn around the declines.  Figure 1 demonstrates that these efforts were somewhat effective in limiting run declines during the 2012-2015 drought, compared to the 1987-1992 and 2007-2009 droughts.

However, the prognosis for 2017 is again bleak.  The consequences of the 2012-2015 drought are about to fully play out.  Once again, projected runs are low and responsible fishery agencies are restricting harvest.  Managers once again must take action to minimize the long term effects and help bring about recovery.

Immediate actions in wet year 2017:

  1. Reduce harvest: Sadly but necessarily, the Pacific Fishery Management Council and west coast states took this first step: they severally restricted the 2017 harvest in the ocean and rivers.
  2. Improve spawning, rearing, and migrating conditions: Sadly, responsible agencies unnecessarily compromised on Sacramento River water temperatures in the first ten days of May, 2017 (Figure 2).  The Bureau of Reclamation released flows as low as 5000 cfs from an effectively full Shasta Reservoir, and water temperature at Red Bluff exceeded the 56oF temperature standards in the biological opinion for salmon and in the Basin Plan.  The resulting high water temperatures affect salmon egg incubation, rearing, and emigration-immigration success.  In one of the wettest years on record, there is no excuse for failure to meet flow and temperature targets in all Central Valley rivers and the Delta.
  3. Limit Delta exports: Delta exports this spring reached unprecedented highs not seen in recent decades, resulting in high salmon salvage rates at the Delta fish facilities (Figure 3).1  With high water supplies in this wet year, there is no need for high exports, especially if it reduces survival of salmon and other native fishes.  If anything, exports should be minimal.

Near-term actions over the coming year:

  1. Transport hatchery smolts to Bay: the transport of millions of fall-run smolts from state hatcheries on the Feather, American, and Mokelumne rivers to the Bay provides higher rates of fishery and escapement contributions and low rates of straying.  Barge transport to the Bay offers potentially lower rates of predation and straying for Federal hatcheries near Redding.
  2. Raise hatchery fry in natural habitats: recent research indicates that rearing hatchery fry in more natural habitat conditions increases growth rates, survival, and contributions to fisheries and escapement.  Raising hatchery fry in rice fields is one potential approach.
  3. Restore habitats damaged by recent record high flows in salmon spawning and rearing reaches of the Central Valley rivers and floodplains: in nearly every river, flooding in 2017 has damaged habitats.  These habitats now  require extra-ordinary repairs and maintenance to ready them again to produce salmon.
  4. With an abundant water supply this year, take further actions to enhance flows and water temperatures to enhance salmon survival throughout the Central Valley: actions may include higher base flows, flow pulses, or simply meeting existing target flow and temperature goals.

In conclusion, managers should take immediate actions to minimize the damage to salmon runs from the recent drought using this year’s abundant water supply.  They should avoid efforts to exploit the abundant water for small benefits to water supply at the expense of salmon recovery and should make every effort to use the abundant water for salmon recovery.

Figure 2. Upper Sacramento River flows and water temperatures in May 2017. The target water temperature for Red Bluff is 56oF. Source of data: USBR.

Figure 3. Export rate and young salmon salvage at South Delta federal and state export facilities in May 2017. The target export rate limit for May is 1500 cfs. Source of data: USBR.

Feather River Chinook Salmon Status

The Feather River has populations of fall-run and spring-run Chinook salmon. Both populations are heavily supplemented (up to 90%) by the Feather River Fish Hatchery near Oroville. There is some natural production in the tailwater below Oroville Dam (Figure 1). The Feather River contributes about 20-25% of the total salmon production in the Central Valley; most are fall-run Chinook.

Figure 1. Lower Feather River and hatchery location. Source: CDFW.

In a recent post I discussed the Sacramento River salmon populations. In this post I discuss the Feather River populations of fall-run and spring-run Chinook.

Fall-Run Chinook Salmon

In recent decades, the fall-run salmon population (returns to the hatchery plus estimates of natural production based on carcass and redd surveys) has had two peaks and one severe low (Figure 2). The peaks were 2000-2003 and 2012-2014. These peak runs were likely the product of wet conditions in brood years 1997-2000 and 2010-2012. Strong hatchery contributions were also important, especially trucking and Bay-Delta pen acclimation of transported smolts in those years. The low population years from 2007-2009 are likely the product of a combination of poor ocean conditions (2004-05), lack of pen acclimation for hatchery fish trucked to the Bay (2003-05), the 2006 winter flood, and the drought of 2007-09.

Figure 2. Fall run Chinook salmon escapement to the lower Feather River and hatchery 1975-2016. No in-river estimates are available for 1990, 1998, or 1999. Data source: CDFW GrandTab.

An analysis of the recruitment-per-spawner ratio in the population over the past 40 years (Figure 3) shows some of relationships described above. The relatively high escapements in periods 2011-2014 and 2003-2006, and the low escapement in 2007-2009, are explainable by river hydrologic conditions as well as ocean conditions:

  1. Recruitment is generally depressed in dry rearing years (conditions during winter-spring two years before spawning year).
  2. Recruitment is generally depressed in dry spawning years (conditions during summer-fall spawning run).
  3. Recruitment is generally depressed for brood years subjected to poor ocean conditions (recruitment years 2007-09 and 2015-16).
  4.  There is no apparent recruit-per-spawner relationship unless the outliers of 2011 and 2012 are removed. This lack of relationship is likely due to the strong role of the hatchery in recruitment. Efforts to improve hatchery smolt survival (i.e., higher hatchery smolt production, trucking, pen acclimation, and other actions) implemented during and after the 2008 “crash” likely helped the 2011-13 recruitment. It is likely that improved ocean conditions also increased recruitment in these same years.
  5. The December 2005 – January 2006 flood and associated rare Oroville Dam “spill” of 2006 may also have depressed recruitment in 2008. Only 1997 and 2017 had similar high spills in 1975-2017 period.
  6. A majority of the years had a replacement rate near 1-to-1 (17 years at center of plot), likely reflecting the stability provided by the hatchery.

Figure 3. Recruitment-per-spawner relationship for Feather River fall-run salmon from 1975-2016 (log10X-4). Numbers show the years in which adult salmon returned to the Feather. The color of the number refers to hydrologic conditions two years previously, when those adults were juvenile fish rearing in the river or hatchery. The color of the circle shows the hydrologic conditions in the year the adults returned to spawn. Blue denotes a wet water year. Green denotes a normal water year. Red denotes a dry water year. Example: Adults that returned to the Feather River in 1983 reared during dry water year 1981: thus, the number is shown in red. 1983, when the salmon returned as adults to the Feather, was a wet year: thus, the circle around the number is blue. The orange rectangle represents poor ocean years. Recruit years 1990, 95, 98, 99, 01, and 02 are missing.

Hatchery Spring-Run

Feather River spring-run Chinook are listed as endangered by the National Marine Fisheries Service. The Feather River spring Chinook salmon run is measured by the number taken into the hatchery (Figure 4). The main patterns indicate stronger runs after 1985-1986, 1993, 1995-1999, and 2010-2012, wetter period that led to stronger runs 2 to 4 years later. Weaker runs occurred after drier periods 1987-1992, 2001-2005, 2007-2009, and 2012-2015.

Figure 4. Feather River spring-run hatchery counts from 1975-2016. Source: CDFW GrandTab.

The spring-run accounting is complicated by inability to count in-river spring run spawners, a problem best described by NMFS:

“The proportion of hatchery-origin spring- or fall-run Chinook salmon contributing to the natural spawning spring-run Chinook salmon population on the Feather River remains unknown due to overlap in the spawn timing of spring-run and fall-run Chinook salmon, and lack of physical separation.”1

An analysis of the recruitment per spawner in the population over the past 40 years (Figure 5) shows some of relationships described above:

  1. Strong showings in the late 1990’s and early 2000’s were likely the consequence of trucking to and pen acclimation in the Bay.
  2. Lesser runs from 2005-2011 were likely a consequence of drier years during spawning and rearing, poor ocean conditions, and lack of trucking and pen acclimation upon release.
  3. The poor run in 2016 was in part due to the start of another period of poor ocean conditions that began in 2015.

Figure 5. Recruitment-per-spawner relationship for Feather River spring-run salmon from 1975-2016 (log10X – 2.5) . Numbers show the years in which adult salmon returned to the Feather. The color of the number refers to hydrologic conditions two years previously, when those adults were juvenile fish rearing in the river or hatchery. The color of the circle shows the hydrologic conditions in the year the adults returned to spawn. Blue denoates a wet water year. Green denotes a normal water year. Red denotes a dry water year. Example: Adults that returned to the Feather River in 1983 reared during dry water year 1981; the number is shown in red. 1983, when the salmon returned as adults to the Feather, was a wet year; the circle around the number is blue.


The Feather River salmon runs are an integral part of the Central Valley salmon population, and make a key contribution to commercial and sport fisheries along the coast of California. The Feather River salmon runs are predominately hatchery runs that benefit greatly from trucking to the Bay-Delta. Trucking and pen acclimation in the Bay prior to release result in good survival to and in the ocean and good returns of spawners to the Feather.

Spring 2017 Delta Fish Salvage

Though it is counter-intuitive in a flood year, fish salvage has become a real problem this spring.

Total Delta exports reached 8,000 cfs in the first week in May, and salvage of salmon and splittail increased sharply (Figures 1 and 2). Normally, Delta standards limit export limits to1500 cfs in April-May in order to protect fish. However, higher exports are allowed when San Joaquin River inflows to the Delta are high. Even higher exports than the present 8,000 cfs are allowed, but the infrastructure cannot accommodate further exports in this wet year (demands are low and reservoirs south of the Delta are nearly full).

Figure 1. Salvage of Chinook salmon at south Delta pumping plants in spring 2017. Source: CDFW.

Figure 2. Salvage of splittail at south Delta pumping plants in spring 2017. Source: CDFW.

In past wet years, there were restrictions on south Delta exports in April and May to protect juvenile salmon, steelhead, splittail, and smelt that were rearing or passing through the Delta.  These restrictions also protected adult and juvenile sturgeon.  Figure 3 shows an example of Chinook salmon salvage in 1999.  The initial peak in February 1999 salvage was salvage of fry (1-2 inches).  The spring peaks were hatchery and river-reared smolts, primarily from San Joaquin River tributaries.  Both exports and salvage dropped after April 15.

In 2017, with the diversion of over half the San Joaquin River’s flow into the south Delta through the Head of Old River and other channels (Figure 4), there is a definite risk that high export levels will draw young salmon and splittail from the San Joaquin into the south Delta.  Once in the south Delta, they are subject to 8,000 cfs of diversions and a mix of tidal flows.  The risk is even higher than it might seem, because the reported State Water Project diversion is a daily average.  Water enters Clifton Court Forebay for only about one third of the hours in each day, during incoming tides.  The reported 5000 cfs is actually more like 15,000 cfs operating for those eight hours, adding to the pull toward the pumps of the incoming tides.

Reported salvage is just the tip of the iceberg, because predators eat up to 90% of juvenile salmon that enter the Forebay before these juveniles ever reach the salvage facilities.

In conclusion, the State Water Board needs to change the Delta standard.  It needs to limit spring exports even when San Joaquin flows are high.  In 2006 (Figure 5), the now-defunct Vernalis Adaptive Management Program limited April through mid-May exports despite high San Joaquin flows.  Salvage was markedly low during this period of limited exports.

If exports continue high through May and June in 2017, there will be detrimental effects on San Joaquin salmon, steelhead, and splittail, as well as on Delta smelt.

Figure 3. Salvage of Chinook salmon at south Delta pumping plants in winter-spring 1999. Note reduction in exports after mid-April. Source: CDFW.

Figure 4. High tide flows in the Delta at the beginning of May 2017. Blue represents positive downstream flows during high tides, where tides had minimal influence. Red denotes upstream tidal flow during incoming tides.

Figure 5. Salvage of Chinook salmon at south Delta pumping plants in winter-spring 2006. Note reduction in exports in early April. Winter-spring San Joaquin flows in 2006 were similar to those in 2017. Source: CDFW.

Shasta River Fall Run Chinook Salmon – Status and Future

In an April 10, 2017 post, I described a sharp decline in the Klamath River salmon runs after the 2012-2015 drought. In that post, I also noted the high relative contribution of the Shasta River run to the overall Klamath run, especially in the past six years. The recent upturn in the Shasta River run and its greater contribution to the overall Klamath run is likely a consequence of efforts by the Nature Conservancy and others to restore the Big Springs Complex of the upper river near Weed, Ca.

The Shasta run has increased measurably since 2010 (Figure 1). Cattle were excluded from Big Springs Creek in 2009, and flows, water temperature and juvenile Chinook densities were markedly improved in and below Big Springs Creek.1 The improved juvenile salmon production likely contributed to greater runs from 2011-2015 and to a higher than expected 2016 run given the 2013-2014 drought (Figure 2). The improvement in the Shasta run bodes well for the Shasta and Klamath runs (Figures 3 and 4). The Shasta run recovery is key to sustaining and restoring the Klamath run and coastal Oregon and California fisheries that depend on the Klamath’s contribution. The Shasta River’s spring-fed water supply comes from the Mt. Shasta volcanic complex. This water supply is resilient to drought and climate-change. The reliability of the Shasta River’s water supply makes the Shasta River’s contribution to Klamath salmon runs particularly important.

Restoration of the Shasta River and recovery of its salmon and steelhead populations has only just begun. Further improvements to the Big Springs Complex, especially to its spring-fed water supply (Figure 5) and to its spawning and rearing habitat, are planned. There is also much potential to improve habitat above the outlet of Big Springs Creek, both in the Shasta River and Parks Creek. There is further potential for habitat restoration in downstream tributaries (e.g., Yreka Creek and Little Shasta River). Reconnection of the upper Shasta River above Dwinnell Reservoir to the lower river would restore many miles of historic salmon and steelhead producing habitat.2 These improvements could make it is possible for the Shasta River to once again produce over half the “wild” (non-hatchery) salmon of the Klamath River.

Figure 1. Fall-run Chinook salmon escapement (spawning run) estimates for the Shasta River from 1978 to 2016. Data Source: CDFW GrandTab.

Figure 2. Mean annual Shasta River streamflow (cfs) as measured at Yreka, CA. Source: USGS. Designated water-year types in this figure are the author’s estimates.

Figure 3. Spawner-recruit relationship for Shasta River. Escapement estimates (log10X – 2 transformed) are plotted for recruits by escapement (spawners) three years earlier. Year shown is recruit (escapement) year. The number is the year that fish returned to the Shasta River to spawn. The color of the number depicts the water-year type in the Shasta River during the year the recruits reared. The color of the circle depicts the water-year type in the Klamath River during the year the recruits reared. Blue is for Wet water-year types. Green is for Normal water-year types. Red is for Dry water-year types. Example: 90 depicts fish that returned to the Shasta River as adult spawners in 1990. These fish were spawned in 1987 and reared in winter-spring 1988. The red number shows that the 1988 rearing year was a Dry water year in the Shasta River; the red circle shows that the 1988 rearing year was a Dry water year in the Klamath River. Note very poor recruits per spawner in 1990-1993 drought period, compared with relatively high recruits per spawner from 2011-2016, even though the latter period included the 2012-2015 drought.

Figure 4. Estimates of fall-run Chinook salmon escapement for the Klamath River, 1978-2016. Data Source: CDFW GrandTab.

Figure 5. Examples of Shasta River monthly average flows as measured at the lower end of Shasta Valley. Streamflow is low from late spring through summer because of surface and groundwater irrigation demands. October flows are higher because the irrigation season (and season of diversion under some water rights) ends on September 30. Data source: USGS Yreka gage.

Scott River Fall-Run Chinook Salmon

In an April 10 post on the Klamath Chinook salmon run, I discussed an expected record low run in 2017.  The Klamath run has six subcomponent runs, including the Scott River.  Improving the Scott River run is one means of improving the Klamath run.

Like the adjacent Shasta and Salmon Rivers, the Scott is a unique ecological gem, sitting high in the Marble and Trinity mountains before plunging north down the volcanic escarpment into the Klamath River canyon (Figure 1).  Like the Shasta River, the Scott flows through a mountain rimmed glacial valley not unlike those in the North American Rockies or European Alps.  Scott Valley is one of those “beautiful places.”  It is also one of the last great places for salmon and steelhead in California.  Unlike the Shasta River whose flow is supported by large volcanic springs from Mt. Shasta, the Scott depends on snowmelt from the Marbles and Trinities, as well as on springs from its alluvial valley.

Figure 1. The Scott River Valley in northern California west of Yreka, CA (Yreka is located in the Shasta River Valley). The Scott and Shasta Rivers flow north into the Klamath River, which runs west to the ocean. The Salmon River watershed is immediately west of the Scott River watershed. The upper Trinity River watershed is immediately to the south of the Scott River watershed.

The Scott River is home to wild runs of Chinook salmon, Coho salmon, and steelhead trout that make up significant components of the Klamath River runs of these species. In this post I address the Scott River fall-run Chinook salmon. The California Department of Fish and Wildlife has estimated the annual run size since 1978 (Figure 2).

Figure 2. Escapement of adult fall-run Chinook salmon to the Scott River from 1978 to 2016. Data source: CDFW GrandTab.

The run size, or “escapement” in fisheries science vernacular, is a consequence of the previous number of spawners; their success; survival of eggs, embryos, fry, and smolts in rivers; survival for up to several years in the ocean; and finally, the success of adults migrating back from the ocean to river spawning grounds. There is a lot that can happen at each of these life stages that may affect the ultimate escapement. I show the effect of several key factors in Figure 3, which starts from the escapement numbers in Figure 2 and shows the recruits-per-spawner relationship.

I hypothesized the following from the Figure 3 recruits-per-spawner relationship:

  1. Recruits-per-spawner is generally higher for wet (blue) rearing conditions – the winter/spring conditions of the year that followed the spawning or brood year. Note that smolts generally reach the ocean by their first summer, so conditions early in their rearing year likely affect survival prior to entering the ocean. Survival may be affected by the rearing conditions in the Scott River and/or those downstream in the Klamath River. Low late-winter and spring flows affect river rearing survival as well as the overall survival during emigration to the ocean. Ocean survival can be a consequence of success during river rearing or emigration: of the smolts that reach the ocean, larger healthier smolts generally survive better in the ocean.
  2. Recruits-per-spawner is generally lower as a consequence of dry conditions during the spawning run (red circle years have lower recruits-per-spawner). The lower Klamath River die-off of adult salmon in 2002 was an example of dry year mortality during the spawning migration.
  3. Recruits-per-spawner may be depressed in very wet rearing years when floods disturb spawning beds of salmon. An example is 1999. The number of recruits was depressed by the 1997 New Years flood, which affected the fall 1996 spawn. Similarly, floods in winter 1982, 1983, 1996, 1998, and 2006 may have reduced survival and run size in 1984, 1985, 1998, 2000, and 2008.
  4. The number of spawners three years earlier has little or no apparent effect on the number of recruits (at least at these levels of spawners). For example: recruits in 2007 and 2008 were relatively high despite low number of spawners three years earlier.

I derived the wet or dry water year designations using Figure 4. I derived the wet or dry August-September streamflow designations for the spawning run from the average monthly Scott River streamflow for those months and years (Figure 5 shows a sample range of years). Note that there is not a lot of difference among years in the August-October flows – they are all relatively low. That is because by August, the snow-melt season is over and base flows are occurring from springs and hay-field and pasture runoff or seepage.

There is also the negative effect on flows from wells and surface diversions, the predominate forms of irrigation in Scott Valley. In the drier years the late summer and early fall river flows exiting the Valley below Ft. Jones can be extremely low (less than 10 cfs – see Figure 5) because of extensive well use, driven by lower available surface water. Low late summer and early fall flows can block salmon from entering the river for several months (Figure 6). This results in loss of stored energy, lower egg viability, and high pre-spawn mortality. It also results in delayed spawning, increasing the likelihood that salmon will spawn in the lower sections of the Scott River, where there is poor spawning and rearing habitat. Low flows in the river upstream can further hinder migration and access to prime spawning tributaries (Figure 7).

It takes about 100 cfs or higher to provide full access to the upper river’s spawning areas. In most years, flows are too low to provide good access. The Scott River Water Trust purchases irrigation water in some years to help the salmon migration. In most years, the river’s baseflows increase soon after the irrigation draw on groundwater ends in late October, allowing unhindered migration.

Part of the solution to the problem of low flows during the spawning run is to cease irrigation earlier. Hay irrigators generally cease pumping water by October 1, and some say there is minimal benefit of irrigating after August. Ranchers often irrigate pastures into November, if only for stock watering. Because many wells are not operated after August, idle wells have sufficient total capacity to readily keep the river watered after September 1 to pump groundwater directly into the river (ranchers would consider this if the costs of pumping were covered). I believe the effect of the extra pumping on groundwater levels would be minimal, because the Valley aquifer recovers from well pumping over the winter-spring recharge season.

Survival during the late winter-early spring rearing and emigration period could be enhanced in drier years by limiting early spring irrigation use and using selected idle wells prior to the irrigation season to add water directly to the river.

In summary, the Scott Chinook fall-run is reduced in dry years when spawning and rearing success are compromised by low river flows in the Scott and Klamath Rivers. The Scott River Chinook salmon population would likely benefit from (1) improved late-summer and early-fall flows that would improve access of spawners to upriver and tributary spawning grounds, and (2) higher river flows in drier years during the late–winter and early-spring rearing and emigration period. A record low run is expected in fall 2017 because of low fall and spring flows in 2015, which limited the survival of the juveniles from the 2014 run.

Figure 3. The recruit-per-spawner relationship for the Scott River fall-run Chinook salmon from 1978 to 2016. Escapement by year (recruits) is plotted against escapement three years earlier (spawners). The escapement values plotted are transformed (Log10X-2). The number shown is the escapement year or recruit year – the year the run was tallied. Number color denotes rearing year water supply type – two years prior to recruit year. Red is dry. Green is average. Blue is wet. Circle represents escapement year water supply during the spawning run (August-September). For example: “04” is run size in fall 2004, which had an average winter-spring rearing year (water year 2002) and dry conditions during the late summer run in 2004 (red circle).

Figure 4. Water years (10/1-9/30) 1978-2016 average annual flow in Scott River measured at Ft. Jones gage. Source: USGS. I designated years above the blue line as wet years, years below the red line as dry years, and years between the lines as average years.

Figure 5. Scott River average monthly flow (cfs) below Ft. Jones for selected years. Source: USGS.

Figure 6. Adult fall-run Chinook salmon waiting at the mouth of the Scott River in the Klamath River in late summer for flows to improve before attempting to migrate up the Scott River to their spawning grounds.

Figure 7. Trickle of flow in the mainstem Scott River in Scott Valley during late summer below Young’s Dam irrigation diversion near Etna, CA. The dam can be seen in the distance at upper center of photo. The fish ladder at the dam is not functional at such low flows. The dam is located approximately 50 river-miles upstream from the river mouth. There is approximately 20 miles of additional Chinook salmon spawning habitat upstream of Young’s Dam.

Longfin Smelt Return from the Ocean

Back in December, I posted that longfin smelt may be gone.  Numbers were way down and early winter 2017 larvae surveys indicated a very poor spawn.  But suddenly in March, larval smelt began showing up in the CDFW 20-mm survey in San Pablo Bay and in the Napa River (Figure 1).  A bunch of adult longfin must have come in from the ocean and surrounding San Francisco Bay with this winter’s very high Delta outflows, and spawned in the Napa River.  While these larval densities are one or two orders of magnitude below previous wet year abundance (1999, 2006, and 2011), they are much higher than those observed in other years over the past decade.  Despite very low recruitment during the recent drought (2013-2015), they were able to muster enough 1-2 year-old adult spawners from around the Bay and nearby ocean to provide a decent spawn in the Napa River.  There appears to be some hope for longfin smelt after all.

Figure 1. Longfin smelt catch densities in March 2017 20-mm Survey. Source : CDFW 20-mm Survey.

Late-Fall-Run Salmon – Status

Late-fall-run Chinook salmon are unique to the Sacramento River. They migrate upstream to spawn below Shasta Reservoir in the Sacramento River in the late fall and early winter. Peak spawning is in the winter months. With emergence in the spring months, juveniles over-summer in the upper river above and below Red Bluff before commencing their smolt migration toward the ocean in the fall, when the lower river cools.

Numbers (escapement) of adults reaching the upper river spawning grounds have been estimated at the Red Bluff Diversion Dam (RBDD) fish ladders, in redd surveys, and in carcass surveys. The counts were accurate until 1991. Beginning in 1992 the RBDD gates were lifted in fall and winter, and ladder counts ceased. Accurate counts were obtained through other methods (aerial surveys, redd counts, and carcass surveys) beginning in 1998. A plot of escapement from CDFW’s GrandTab file (Figure 1) also shows the contribution of the Coleman hatchery returns in the escapement total. The inaccurate escapement estimates from the 1992-1993 fall/winter to the 1996-1997 fall/winter show clearly in Figure 1.

Keeping the accuracy of the counts (escapement estimates) in mind, I plotted recruits vs spawners (escapement vs escapement three years earlier) using the GrandTab totals for all years except 1992-1999, the years affected by the inaccurate estimates from 1992 to 1996. Figure 2 depicts the spawner recruit relationship with year labelled being the first rearing year (freshwater phase) for the recruits. A positive relationship between spawners and recruits is depicted with higher recruits per spawner in wetter rearing years. Wetter years generally have the following survival attributes:

  1. Better spawning conditions – higher flows, more gravel spawning habitat.
  2. Better incubation conditions – less redd stranding, better redd survival.
  3. More floodplain rearing habitat for fry.
  4. Less predation on juveniles from spring through fall.
  5. Better water temperatures spring through fall in rearing reach.
  6. Improved fall emigration conditions (flows, water temperatures, less predation, improved passage in the lower river and Bay-Delta).

Recruitment has been consistently low in recent drought years, which lacked the positive benefits I listed above. Removal of the RBDD gates after 1992, screening of large diversions, and more protective habitat conditions (flows and water temperatures) likely contributed to the population resurgence in the wetter year periods from 1995-2006. However, the droughts years from 2007-2015 have driven the population to such a low level that the run is now primarily sustained by hatchery production.

A recent assessment by CDFW1 recognizes the roles of these stressors on the late–fall-run salmon population. I quote from the assessment and comment below.

The effects of RBDD were more subtle. This dam apparently delayed passage to upstream spawning areas and also concentrated predators, increasing mortality on out- migrating smolts. Kope and Botsford (1990) documented that the overall decline of Sacramento River salmon was closely tied to the construction of RBDD. Raising the dam’s gates for much of the year to allow salmon passage apparently alleviated much of this problem. The gates are now open year-round, allowing uninhibited passage of adult and juvenile late fall-run Chinook salmon.

Comment: Eliminating the RBDD migration blockage and predator hotspot was important, but it also allowed predator access to the upper river in the spring-fall rearing period. The numbers of river spawners has continued to decline while the proportion of hatchery returns increases.

“Fish from Coleman National Fish Hatchery on Battle Creek are contributing at a low rate to the spawning population in the mainstem Sacramento River.”

Comment: The rate is no longer considered low. The population’s viability is in question with the large contribution by the hatchery.

Large pumping stations in the southern Sacramento-San Joaquin Rivers Delta (Delta) divert approximately 40% of the historic Delta flows, resulting in substantial modifications in flow direction (Nichols et al. 1986). Pumping also increases the likelihood of out-migrating smolts entering the interior delta, where longer migration routes, impaired water quality, increased predation, and entrainment result in higher mortality rates (Perry et al. 2010).

Comment: Wild and hatchery-released smolts move downstream toward the Delta with the first fall rains (Figure 3). Those that reach the Delta before the end of December are subject to an open Delta Cross Channel and high exports (Figure 4), and high rates of predation, which together likely contribute to the very low return rate of the late fall hatchery and wild smolts, especially from drier years.

Hatcheries. Late fall-run Chinook salmon have been reared at Coleman National Fish Hatchery on Battle Creek since the 1950s, even though the run was not formally recognized until 1973 (Williams 2006). The current production goal is one million smolts per year, which are released into Battle Creek from November through January (Williams 2006). Hatchery broodstock selection for late fall-run fish includes both fish returning to Coleman National Fish Hatchery and those trapped below Keswick Dam. Large numbers are needed because survival rates are low (0.78% at Coleman).

Comment: The return rate of late–fall-run smolts from Coleman as adults to sport and commercial fisheries is among the lowest from Central Valley salmon hatcheries (Figure 5), despite late–fall-run smolts being the largest hatchery smolts at release.

A wide array of actions have been prescribed for Central Valley listed winter-run and spring-run salmon and steelhead in recovery plans and biological opinions that will also benefit late fall salmon. Actions include improving spawning and rearing habitats, as well as river flows and water quality. Among these are a specific set of actions that would contribute most to the late-fall-run recovery:

  1. Do not release Coleman late fall hatchery smolts until after the first winter rains when the Delta Cross Channel is closed and Delta exports are limited by the NMFS OCAP biological opinion. (Present plans call for early January hatchery releases, whereas past releases were also made in November and December.)
  2. Provide a coincident flow pulse from Shasta Reservoir to the first downstream tributary rain pulse to stimulate wild late-fall-run smolt emigration from the Redding reach below Shasta/Keswick.
  3. In the event of significant natural fall flow pulses that stimulate emigration of wild late–fall-run smolts from the upper river, add releases of pulse flows from the Feather and American rivers, close the Delta Cross Channel, and reduce Delta exports to enhance passage to the Bay and Ocean.
  4. In drier years with minimal fall-winter rains, consider barging late–fall-run hatchery smolts from Knights Landing on the lower Sacramento River above the Feather River to the Bay. Straying problems identified for truck-transported late–fall-run hatchery smolts may be reduced with this approach, while markedly increasing smolt survival to the ocean. Maintaining the barge route to Sacramento water on the west side of the river may minimize imprinting (and subsequent straying) to the Feather and American rivers.

Figure 1. Late-fall-run Chinook salmon escapement estimates to upper Sacramento River 1974-2014. “Wild” means counted in the river not at the hatchery. Wild spawners may include a high proportion of hatchery origin adult salmon. Source: CDFW GrandTab.

Figure 2. Spawner-recruitment relationship for late-fall-run Chinook salmon in the upper Sacramento River below Shasta Reservoir. Numbers are Log10 -2 transformed. Year numbers are for rearing year in freshwater. For example: 99 dot represents rearing year when spawners from 1998-1999 returned as recruits in 2002-2003. Red bold designates critical water year. Red non-bold designates dry water year. Green bold is above-normal water year. Green non-bold is below-normal water year. Blue number is wet water year. Relationship is significantly positive with higher recruitment per spawner in wet years.

Figure 3. Screw trap large salmon smolt catch at Knights Landing fall-winter 2000-2001 to 2002-2003. Also shown is lower Sacramento River flow at Wilkins Slough gage. Source: CDFW

Figure 4. Salvage of young salmon at Delta export facilities from August 2015 to March 2016. Also shown is Delta inflow and outflow, and export rate. Red circle highlights late-fall-run salvage period with green dots being late–fall-run hatchery smolts. (Source: CDFW)

Figure 5. Return rate in sport and commercial fisheries of tagged Central Valley hatchery salmon. CFHLh denotes late fall releases at Coleman hatchery. Other release locations are Feather River (FRH), American River (NMF), Mokelumne River (MOK), Merced River (MER), and Sacramento River (Sac). W denotes winter-run, S spring-run, and F fall-run. tib denotes Tiburon, t denotes trucked, and h denotes hatchery site release. Source: CDFW.

Discussion on Delta Smelt

This past November’s science conference on the Bay-Delta included a discussion on Delta smelt.1 Some of the discussion points are presented in this post, with my comments.

The Delta smelt is adapted to an ecosystem that no longer exists. “Looking at the Delta smelt’s life history, their adaptations, their tolerances to different environmental conditions, and looking at the landscape of the Delta, that the state that the estuary is in now basically does not favor the continued existence of the species. Looking at its physiology or biology, it’s no longer adapted to this particular ecosystem, as we’ve progressively changed things through time.”

Comment: Delta smelt remain highly adapted to the Bay-Delta Estuary. However the habitats are so disturbed, especially during droughts, that little recruitment is possible, resulting in a long term decline in the adult spawning population that may not be reversible. Wet years and improved water management could possibly reverse this pattern and bring population recoveries, similar to those in 2010 and 2011.

There is no smoking gun. The proximate causes of the decline are interactions among multiple factors that have altered their habitat, making it increasingly unsuitable. “Looking at all the drivers that are associated with their population status, it doesn’t really appear to be a single smoking gun,” said Dr. Hobbs. “In each particular year, that there could be a series of different drivers that creep up that could basically lop off the population at any given time, and every year it could be somewhat different at different spatial and temporal scales, so it makes it really difficult to really point the finger at one particular driver, at least as the way the data was presented and analyzed in different papers.”

Comment: In nearly every case the “smoke” emanates from poor water management in dry and average water years, when Delta inflows, outflows, and exports are manipulated in ways that disturb the ecosystem. The other factors are simply secondary reactions to the gun’s discharge.

The population exhibited some resilience when in 2011, environmental conditions were good and abundance was at near historic levels, but unfortunately the current drought may have eroded such resilience. “In 2011, we saw good flows and cold temperatures, particularly through the summer and fall, and we got a pretty large return in adult abundance that year, so up through that time period, it appears that even though the population abundance was declined, the population still had the capacity to return, so there was still some resilience left in the population,” he said. “With this ongoing drought, we may be getting to the point where the population resilience is now reaching a point where it may not be able to return to previous levels if we give it the right environmental conditions only over a single generation. What’s really important for the species being annual is that it has to have consistent conditions, not for a single year, but for many, many years.”

Comment: It is not a matter of resilience. It is simply a matter of survival and recruitment, and maintenance of a viable spawning population. It is not the drought, but how the water management rules were weakened in the drought. In drought, the rules must be enhanced and enforced, not weakened, to protect the species.

The continued decline of the Delta smelt demonstrates the general failure to manage the Delta for the coequal goals of maintaining a healthy ecosystem while providing a reliable water supply for Californians. Dr. Hobbs noted that this was something that was debated amongst the authors. “When the idea of the coequal goals was brought up, it was a great idea, but if you think about it, it was being implemented at a time when we were already taking close to 90% of the freshwater out of the estuary, so the fish were already well behind the curve,” he said. “We basically came out and said, ‘we’re try to manage coequally,’ and we weren’t really at a 50/50 state at that point. We don’t seem to have the capacity to bring this back to a level where it could be a 50/50 share between water for people and water for fish.”

Comment: This is just simply confusing. Coequal protection of beneficial uses does not mean that fish get 50% of water and other uses get 50%. And someone would have to be a little more precise in defining 50% (or whatever percent) of what. Fish have basic needs that protect them from extinction. Water management must work around these needs. The problem is most acute in dry years and droughts. But better allocation of water is needed in all years so enough is available at least for triage of all uses in multi-year droughts.

“We sort of put it in the terms of the coequal goals, but it’s really a failure of all of us, I think, said Dr Hobbs. “I take a lot of personal responsibility for the failure because we have a lot of science that takes a long time to get out and communicate to the public and some of that information could really be implemented on a much more rapid scale. I know a lot of other folks I talk to feel sort of responsible too because it’s under their guise to try to manage and protect the species, and we’ve continued to fail. And honesty longfin smelt is right behind them.”

Comment: The responsibility for this grand failure does not lie with the scientists. It lies with the water managers and the agencies who compromised in negotiations on water rights, water quality standards, and biological opinions. Co-equal goals does not mean “cutting the baby in half.” It means equally maintaining the viability of the two beneficial uses, which obviously does not happen.

Moderator Randy Fiorini asks Paul Souza (USFWS): “What did you find usable in this report, which represents the best available science?” “I think it’s extraordinarily helpful in terms of a synthesis of where we stand with Delta smelt,” Mr. Souza answered. “Clearly we’re in the emergency room. This is a species that has had a precipitous decline, it’s on the brink of extinction, and in situations like this, it becomes extraordinarily challenging.”

Comment: Yes it is very difficult to revive half a baby. The important thing is to keep the next baby, if there is one (however small), alive and healthy. If there is, maybe we can make an extra effort in nurturing it to adulthood.

“One of the things that I learned from this work is that there is no silver bullet,” Mr. Souza continued. “There are a lot of different activities that must be accomplished, which makes it truthfully more difficult. The more standard situation for very imperiled species is that you have one significant driver that you can address – for example habitat loss for terrestrial species.”

Comment: There most certainly is a “silver bullet,” but it is made of H2O.

“The Delta smelt, clearly as described in that paper, is among the most imperiled species in the country,” Mr. Souza said. “I think it’s important to also understand that it has as much political attention as arguably any species in the country as well. The situation is truly an interesting one from a conservation perspective. We have a very small fish that’s had a dramatic decline that is in the heart of the water supply for the biggest state in the union, and also provides water obviously for agriculture which is among the most productive in the world. So with that, and all of the development pressures that we’ve seen, we have this unique complex situation to deal with.”

Comment: This is exactly why the Endangered Species Act was enacted. Are we going to protect the largest and most important estuary in California and the western United States or not?

“Going back to the real challenges that the paper describes, we have to figure out how to make incremental progress in the face of uncertainty, and the Delta smelt resiliency strategy is something I’m very excited about,” Mr. Souza said. “I want to give kudos to the State of California for the leadership they’ve provided. It outlines 13 different activities that we think could be helpful in that regard. So truthfully, I’d love to hear from you, Jim, among those 13 activities, which would you prioritize, and why, and which do you think are going to be most promising to help the species get in a better condition?”

Comment: If the Strategy outlined was so exciting, why wasn’t any of it implemented in 2016? The Strategy simply is cutting the baby into thirds.2 “Kudos” to the State for simply recognizing its long-held responsibility.

“I think the number one thing that we should do is to address the outflow issue,” responded Dr. Hobbs. “We need to think hard about what kind of outflow, when, where, and what kind of intensity. The work that was done by Ted Sommer this summer, collaborating with some of the ag folks and getting water down the Toe Drain of the Yolo Bypass was the lowest hanging fruit. Very little water was needed to necessarily get that productivity moving from the Toe Drain into the North Delta arc area. I think that’s the place we should start, considering the state of affairs with the amount of water we have.”

Comment: Yes, water is the silver bullet in the form of Delta outflow. Think of Delta outflow as the powder charge that delivers the silver bullet. However, a little bit of hot, dirty, ag water in summer from the Yolo Bypass is not3 much powder. Prejudging the amount of water available and needed is also not a way to start.

“We’re probably going to have a little bit of water to do summer flow pulses or fall flow pulses so we need to think really strategically about where we put that water, rather than just putting it down the middle of the Sacramento River where 200,000 acre-feet will hardly be even measurable,” said Dr. Hobbs. “If we put this in novel places, we might be able to create the habitat conditions that will be supportive of the species.”

Comment: Why just summer or fall? Why just pulses? 200 TAF of water down the Sacramento River or 1000 cfs for 100 days is a lot of water, which would provide measurable benefit to the river, Delta, and Bay particularly in a dry year. And why just 200 TAF, when ag takes more than 10,000 TAF?

“Coming back to the Yolo Bypass issue, some of the work we’ve been doing recently is that there are a large number of Delta smelt actually residing in the Toe Drain area for a long period of time, and some even staying over the summer and becoming full freshwater resident fish living in that habitat, so that region is clearly one of the most important areas for smelt right now,” said Dr. Hobbs. “We do have the capabilities of providing what water we can provide in that particular habitat, so that’s where I would start.”

Comment: There is no evidence that smelt survive the hot summers in the Yolo Bypass or in the Delta. The most important action is to keep the low salinity zone habitat of the smelt downstream of the Delta in Suisun Bay with more outflow in drier years. 250 TAF of water (see next quote) could help do this in many years.

“Of the 13 provisions in that Delta smelt resiliency strategy, the one that’s probably going to be the most challenging, the most costly, and the most controversial would be the outflow test of 250,000 acre-feet of water,” said Mr. Souza. “We know that water is a precious commodity; there is no free lunch. If that water is acquired for a test, it’s going to come with some tradeoffs.”

Comment: Why is water not available to maintain key beneficial uses protected by State laws, and why is it not free? Why is more of the natural flow being allocated to water rights each year? Why isn’t water used for human use not taxed like the State’s carbon tax to help purchase more water rights and restore more habitat lost to development? Why aren’t the co-equal goals to protect the environment being addressed?

“That really is the place that I find fascinating in the work that we do,” said Mr. Souza. “It really is the interface of science and policy. How do you make these choices, and similarly, how do you get meaningful results from these 13 different tests that are going to allow us to get better? That is really all that we can ask of ourselves is try to get a little better and to try to make some incremental progress in the face of these extraordinary challenges.”

Comments: A “little better” and “some incremental progress” are not going to cut it. The interface of science and policy is longstanding: it is the policy and management that have prioritized the water supply side of resource allocation.

“I’d love to get your thoughts, Jim, about how we actually measure success,” said Mr. Souza. “These 13 actions I think are all important and I’d love to see them all done as fast as possible. Clearly some are easier than others, some more costly than others, but one of the things that I’m already seeing as a significant challenge is how do we know if they are making a difference? When you have a species that is in such a precarious position that’s so hard to find, how can you craft goals and objectives at the population level that we can then implement these 13 provisions and actually measure whether there’s a biological response that is meaningful and a result of the actual test themselves?”

Comment: There are a dozen metrics that provide a measure of smelt performance. These metrics have been available for a decade or more. For each identified action, managers could apply one or more of these metrics to numerically assess the response in the smelt population.

“I think we have the tools to do that,” said Dr. Hobbs. “We have a strong scientific group of people here who have a diverse set of skills. We have really nice conceptual model and a good synthesis of Delta smelt biology. We could use that framework with those strategies in an adaptive management context and look at each of those things that we’re going to do, and with the scientific community come up with the measurable objectives.”

Comment: the tools and metrics are well developed, but objectives are lacking, as are measures that protect the smelt and their habitat.

“In some of those situations, we may not be able to measure the response in Delta smelt themselves, but we could look at the conceptual model and look at different parts of that system for positive results,” said Dr. Hobbs. “For instance, this summer we saw a decent phytoplankton bloom that was associated with water coming down the Toe Drain and some zooplankton production. We are going to have to rely on the fish being able to respond and if they are at such low abundances that we don’t see a population level response in our surveys, maybe we need to be including additional types of monitoring in adaptive scientific field experiments and searches for Delta smelt in these places so that we can do this. The Yolo Bypass is monitored by DWR, but we don’t really have a broader concerted resource to go after doing this on the real time scales that we actually need to do be doing it.”

Comment: The bloom mentioned was minor and occurred where there were no smelt. At the same time, a larger independent bloom occurred downstream in the low salinity zone as a result of classic estuary dynamics (an unrelated pulse of outflow4), along with a recent high abundance of young smelt triggered by wet year Delta hydrodynamics.

“Specifically referring to the recovery plan, there were a series of actions that were discussed, and really none of them were really done,” said Dr. Hobbs. “That was probably because at the same time, the Bay Delta Accord was being put into place to manage flows and to keep the low salinity habitat in the right place in Suisun Bay for a certain amount of time, and that was part of that plan. It wasn’t specifically the main objective and it wasn’t the only thing that was being recommended, but because we were coming together and forming this California and federal coalition to address the issue, I think a lot of effort was put there on that particular issue.”

Comment: Much of the Recovery Plan was not adopted or updated over the past two decades based on performance. The key specified action in the plan was simply keeping the low salinity zone in Suisun Bay rather than upstream in the Delta. Instead, dry water year water allocations were almost entirely allotted to water supply, to the detriment of ecosystem.

“I’ll first make the point about recovery plans,” said Mr. Souza. “They do a wonderful job of bringing scientists together, and if they are really strong, they actually bring policy makers together and the regulated community together and identify a blueprint for going forward. What they don’t do is appropriate funding. And so there are lots of plans that have been put together that have never had the capacity to have full implementation; that’s just the reality of conservation wherever we are.”

Comment: I am not sure about this general statement. The problem really is the plans – they do not provide the protection the smelt need. The Recovery Plan and water quality standards are over 20 years old. The OCAP biological opinion in 2008 lacked adequate protections and is being revised.

“There is a real danger in threatened and endangered species conservation and ecosystem management more broadly speaking, when we focus too much on a single species,” he continued “We in the Fish and Wildlife Service have been criticized in the past for single species management to the detriment of other species. We’re at our best when we’re thinking about the ecosystem and multiple species and trying to find the optimization of habitat conditions for them, not the maximization for any one in particular.”

Comment: This is really a bad excuse for not protecting the Delta smelt, which was originally chosen as the “canary in the coal mine” for the Bay-Delta and all its species. I know of no species hurt by smelt protective actions, but many that benefit from them.

“We really need to focus on the tone of the conversation and how we talk about Delta smelt, and I would really love to recast this as a conversation about the Bay Delta and a shared vision,” said Mr. Souza. “The best most important conservation successes that I’ve seen in my career are grand compromises where we sit down with the affected community, we have a focused conversation about the needs of agriculture, and municipalities, and wildlife, and their habitats, and we again maximize none of those interests but do our best to optimize all of them.”

Comment: I have been involved in such sit-downs for the Delta for 40 years. I have seen many grand compromises that keep cutting each reboot of the Bay-Delta in half. One half to the tenth power is a tenth of one percent. There is no optimizing for all. Something has to give.

“We have to foster a community where we’re all in this together, because we all love the same resource, and it’s extraordinarily precious to all of us,” said Mr. Souza. “Only together are we going to be able to find a path forward where we’re doing the best that we can for this ecosystem, and it needs to move beyond a conversation where people are pitted against wildlife. That is a losing proposition for conservation and I challenge all of us to help be a part of that more positive dialog.”

Comment: We all do not share the love for “the little three inch fish”. I doubt the new Secretary of the Interior will share the love that Mr. Souza holds for Delta smelt.

Question from the audience: “I greatly appreciate your comment that single species management is almost certainly not going to be effective as multispecies ecosystem management, but I think one of the frustrations that we have all experienced in this particular system is that regardless of whether we’re using the science to inform single species management, or using the science to inform multispecies ecosystem management, is that the science is presented and recommendations are made but in fact actions are not taken. Many times the scientific advisory boards or councils or workgroups that advise specific actions and the agencies chose not to do it, so I’d like to you to respond to this relationship between the science and the decision making?”

Comment: Great question.

“My first reaction to it is that science is the foundation of decision making that’s strong for conservation,” responded Mr. Souza. “But in nearly every instance, there are ten policy legal choices that can be made with the same science, and so the real art for a policymaker is figuring out how to use that science in a way that not only is going to address the issue of the moment, but is going to be strategic in helping to facilitate the kind of relationships necessary to do something bigger together in the future than any of us could do alone.”

Comment: My, my. Enough from Mr. Souza.

Sacramento River Fall-Run Salmon – Status and Future

Have poor ocean and river conditions during the recent 2012-2015 drought contributed to a collapse of the Sacramento fall-run salmon population as they did during the 2007-2009 drought? Has trucking hatchery smolts to the Bay in the recent drought helped maintain the fall-run population?

I discussed these and related topics for the San Joaquin River fall-run salmon in a post on February 13. In this post, I turn to the Sacramento and its tributaries.

In a March 1 post on its daily blog, the California Department of Fish and Wildlife predicted poor salmon runs this year:

Chinook that will be harvested in ocean fisheries in 2017 hatched two to four years ago, and were deeply affected by poor river conditions driven by California’s recent drought. CDFW and federal fish agency partners have expended millions of dollars on measures to minimize the impacts of the drought. These efforts have included trucking the majority of hatchery salmon smolts to acclimation pens in the lower Delta, improving hatchery infrastructure to keep juvenile fish alive under poor water quality conditions and partnering with sport and commercial fishermen to increase smolt survival. Though all of these efforts helped, other environmental factors – such as unusually warm water conditions in the ocean – were beyond human control.

While CDFW’s statement is true for the most part, and many of the Department’s efforts were commendable, there are additional factors that also were important:

  1. Water management strategies during the drought that prioritized water supply over salmon greatly affected river conditions, especially in mainstem rivers (Sacramento below Keswick, lower Feather, and lower American). Adult salmon and egg/embryo survival were compromised by warm, low flows below dams.
  2. Many of the hatchery trucks released their smolts in the Delta near Rio Vista rather than in the Bay. Many smolts were also released near the hatcheries. Both measures led to higher predation on smolts in the warm, low river flows that were characteristic of the drought years.
  3. There were many factors that were within human control that contributed to poor salmon survival and production. Chief among these was the failure to maintain prescribed flows and water temperatures below dams. Flow and water temperature prescriptions to protect fish were weakened during the 2013-2015 critically dry water years.

There was ample evidence and known circumstances that another population collapse was possible. Such evidence included the limited recovery during the wetter 2010-2012 sequence, and the effects of the 2013-2015 drought had begun to show (Figure 1). Most notable was the sharply lower number of spawners returning in 2015. Brood year 2014 spawners produced very low numbers of young in the winter-spring of 2015.1

A close look at recruitment per spawner in the population over the past 40 years (Figure 2) provides clear evidence that recruitment suffers in dry winter-spring rearing years or dry fall spawning years. These factors overwhelm the background relationship between spawners and recruits three years later. Patterns in Figure 2 indicate:

  1. Recruitment is significantly depressed in drier years compared to wetter years. The major contributing factor is likely poor survival of juveniles in winter-spring of their first year.
  2. Recruitment is severely depressed for brood years rearing in critical years and returning as adults two years later in critical years (e.g.,1988-1990, 2007, 2013).
  3. Recruitment can be depressed for brood years with good winter-spring juvenile rearing conditions but poor conditions before adults return (e.g., 2005, 2006).
  4. Recruitment can be enhanced for brood years with poor winter-spring young rearing conditions but very good fall conditions for returning adults (e.g., 1994).
  5. There may be an underlying positive spawner/recruit relationship, but it is overwhelmed by the effect on recruitment of flow-related habitat conditions.
  6. Poor ocean conditions in 2005-2006 likely contributed to poor recruitment.
  7. The increase in the relative contribution of hatchery fish is a concern2 as is the declining contribution of mainstem spawners (see Figure 1). With estimates that up to 90 % of the spawning population are fish of hatchery origin, and very little evident genetic diversity, the population is already nearly totally dependent on hatcheries. California sport and commercial salmon fisheries, which depend for the most part on the fall-run salmon, will remain dependent on fall-run hatcheries well into the future.

Present enhancement efforts will help sustain the population and fisheries. Habitat restoration and improved spawning-rearing-migration conditions (flows, water temperatures, and physical habitat) will help increase natural production. Upgraded infrastructure, improved transport (i.e., trucking and barging), and hatchery fry floodplain rearing could improve hatchery contributions. Improvements in hatchery and natural population genetic diversity would help sustain healthy populations into the future.

Figure 1. Sacramento River fall-run Chinook salmon spawner abundance (escapement) from 1975 to 2015. Source: CDFW GrandTab.

Figure 2. Sacramento River spawners versus recruits three years later from escapement estimates (Log10X – 4 transformed). Note that some variability likely occurs from a low number of 2 and 4 year-old spawners in the escapement estimates. Numbers are sum of hatchery, mainstem, and tributary estimates from CDFW GrandTab database. Number shown is rearing year (winter-spring) following fall spawning year. For example: “88” represents rearing year for 1987 spawning or brood year. These fish returned to spawn (recruits) in 1990. Bold red years are critical water years. Non-bold red years are dry water years. Blue years are wet water years. Bold green years are above-normal water years. Non-bold green years are below-normal water years. Red circles represent adult return years being drier water years. Blue circles represent return years being wet water years Green circles represent return years being normal water years. Orange square denotes rearing years with poor ocean conditions.

2017 Klamath Chinook Run – “Disaster or Catastrophe?”

The Klamath River Chinook salmon fall run is expected to be a record low in 2017.1 Predictions are near or below the record low run in 1992. These record low runs followed extended droughts from 2013 to 2015 and 1990 to 1992, respectively.

A very low run in 2016 prompted the Yurok Tribal Council to cancel its commercial fishing season to protect future fish populations. The 2016 salmon allocation was the second lowest on record, and failed to provide each tribal member a salmon. The Tribe did not serve fish at the annual Klamath Salmon Festival for the first time in the event’s 54-year history. In January 2017, the federal government issued a disaster declaration for the 2016 Yurok Tribe fishery.2

An April 6, 2017 article in the Eureka Times Standard stated:

  • Tribal fishery scientists such as Michael Belchik of the Yurok Tribe stated the low return of spawners is the result of several severe years of drought conditions and river management practices, which caused the waters to warm and become hot beds for toxic algae and deadly parasites. In 2014 and 2015, up to 90 percent of juvenile Chinook salmon on the Klamath River are estimated to have died from an intestinal parasite, believed to be a major cause for this year’s low run, as were poor ocean conditions…. “All these things together conspire to create a real catastrophe for fisheries,” Karuk Tribe Natural Resources Policy Advisor Craig Tucker said.
  • Organizations see dam removal and changes to the federal government’s management of the river as being key solutions to the underlying causes of this year’s low salmon return.” “The solution for this problem is to remove the Klamath dams now,” Pacific Coast Federation of Fishermen’s Association Executive Director Noah Oppenheim said.

A Yubanet article described the expected ancillary effect on the whole California coastal fishery:

The disaster stems from a crash of Klamath salmon stocks, but in order to protect the few Klamath fish that are in the ocean, fisheries regulators have little choice but to close or nearly close the economically valuable commercial and sport fishing seasons along the length of the Northern California and Oregon coastlines. This will impact tribal and non-tribal families alike.

CDFW stated: “Chinook that will be harvested in ocean fisheries in 2017 hatched two to four years ago, and were deeply affected by poor river conditions driven by California’s recent drought.”

A UC Davis study placed some of the blame on hatcheries. “My results suggest that hatcheries’ harm to wild salmonids spans the entire Klamath River basin. For fall Chinook salmon, the decline is concurrent with increases in hatchery returns – a trend that could lead to a homogenous population of hatchery-reared Chinook”.

Having been involved in the Klamath River for 40 years, I provide some of my own insights in this post. In follow-up posts, I will take a closer look at the Scott and Shasta rivers, the two main salmon tributaries of the upper Klamath that contribute substantially to the overall upper Klamath salmon run.

A summary of the overall Klamath salmon run escapement numbers or spawner estimates for the past 40 years is shown in Figure 1. The spawning numbers in 2016 were low, yet this drop came only two and four years after near record runs. Contributions for all six upper Klamath subcomponents in 2016 were down substantially from 2014. Predictions of a poor run in 2017 come from the low number of two-year-old “jack” salmon in the 2016 spawning run.

The question is: why did the strong run in 2014 produce the expected record low run in 2017? And why did the strong run in 2012 produce the weak run in 2015? And on the flip-side, why were the runs in 2012 and 2014 so strong, especially given they occurred during the recent multiyear drought?

A close look at the spawner-recruit relationship (Figure 2), how recruits are related to the number of spawners three years earlier, provides further insight into factors controlling long-term recruitment.

  1. The spawner-recruit relationship is weak at best, reflecting the fact that estimates might be poor and/or that other factors are more important than just the number of spawners. The 1995 recovery after the record low 1992 run provides compelling evidence that survival and recovery can be strong even from the weakest of runs (with strong hatchery support – see hatchery component for 1995 in Figure 1). Unfortunately, 2017 appears to suggest that strong runs can produce very weak returns three years later if other factors such as drought are dominant.
  2. The population crashes (2016, 2004, 1992) occurred after multi-year droughts (Figure 3). Multiyear effects compound changes to sediment, pathogens, and water quality, the suggested causes of these crashes.
  3. Population expansions (2012-2014, 2007-2009, 2000-2003, 1995-1997, 1985-1988) occur after a series of wetter years.
  4. There may be some underlying effect of floods, as indicated by the poor run in 1999, a consequence of the New Year 1997 flood that washed out the fall 1996 spawn.
  5. The poor run in 2016 and the expected record low run in 2017, in addition to the effects of the 2013-2015 drought, may have been affected by poor ocean conditions, as was believed to be the case in the poorer than expected 2004-2006 runs.
  6. Several factors potentially affect production or survival per spawner: conditions during the spawning run (flows, water temperature, disease, upstream passage hinderances, etc), first year rearing and emigration conditions (flows, water temperature, predators, prey, disease, toxins, etc), and ocean conditions. It is likely that flows throughout the water year (Figure 4) have some effect on survival of the affected or subsequent brood years.
  7. The contribution of the Shasta River appears to have increased in recent years, likely as a result of the Nature Conservancy’s efforts at Big Springs (more on this in an upcoming post).

Overall, the droughts of 1990-1992 and 2013-2015 (Figure 3) were likely the single most important factors in the upper Klamath Chinook salmon population dynamics. The role of the Irongate Hatchery contributions seems relatively stable and a likely important contributor to recoveries after drought. I was unable to determine the contribution of hatchery salmon to the other components of the run, but it is likely a large factor in the Bogus Creek and upper Klamath elements. It is possibly a lesser factor in the Salmon, Scott, and Shasta river elements, which speaks to the importance of these potentially “wild” runs.

In closing, some thoughts on potential solutions:

  1. Knowing a good run was occurring in drought year 2014, managers could have done more to protect the spawners, eggs-embryos, and subsequent rearing-emigrating juveniles with better flows and water quality. Perhaps the recent federal court decision may help ensure future protections. In poor water supply years like 1990-1992 and 2013-2015 (Figures 3 and 4), water managers simply must provide protections for salmon.
  2. Future removal of the four dams may help reduce the adverse multiyear effect of droughts on disease and water quality and may provide additional spawning and rearing habitat.
  3. Much more could be done to increase run components from the Scott and Shasta rivers (more on this in upcoming posts).
  4. The hatchery program is long overdue for reform and upgrade. The program should shift from production to conservation of fall-run and spring-run Chinook, Coho and steelhead.
  5. These and other suggestions are discussed in a prior post.

Figure 1. Chinook salmon escapement estimates to the upper Klamath River including Irongate Hatchery, Bogus Creek, Scott River, Salmon River, Shasta River, and Klamath River mainstem below Irongate Dam. The preliminary prognosis for fall 2017 total escapement is 11,000. Source: http://www.pcouncil.org/salmon/background/ document-library/#EnvironmentalAssessmentsalLib

Figure 2. Spawner-Recruit relationship for upper Klamath River fall-run Chinook salmon population. The number is the transformed (log10X – 3.5) escapement estimate for the fall of that year as shown in Figure 1. The color represents winter-spring hydrology conditions in the Klamath River two years earlier when this brood year was rearing in river habitats. Red is dry, green is intermediate, and blue is wet (from Figure 3). Circle color represents late summer water year conditions in numbered year. For example: year 92 represents the recruits in fall 1992 from brood-year 1989 spawn that reared in 1990 winter-spring (red dry year); the red circle represents dry conditions in late summer of that water year (1992). Note that the spawning run for 2002, the year the large die-off of adult salmon occurred in the lower river due to low flow and high water temperatures, likely contributed to the poor returns (recruits) in 2004 and 2005.

Figure 3. Average annual discharge by water year (10/1-9/30) of Klamath River as measured at Link River near Klamath Falls, Oregon. Data source: https://waterdata.usgs.gov/nwis/ annual?site_no=11507500&agency_cd=USGS&por_11507500_113138= 545477,00060,113138,1962,2017&year_type= W&referred_module=sw&format=rdb

Figure 4. Monthly average flow (cfs) in Klamath River below Irongate Dam in selected years. Year 2011 was a wetter year. Year 1992 was a critically dry year. Years 2002, 2005, and 2013 were dry years. Year 2016 was an intermediate water year. Source: www.waterdata.usgs.gov.

Reclamation Requests Higher Smelt Take Limits

The State and Federal water projects requested on March 16, 2017 a higher take limit for Delta smelt under their endangered species permits for the south Delta pumping plants. Under the present pattern, it appears that the take limit set in the 2008 Delta Smelt Biological Opinion may soon be exceeded. The request states:

“Although mechanisms underlying recent salvage events are unknown, some possibilities include relatively high turbidity throughout the Delta over an extended period of time leading to increased movement; broad distribution and/or high survivorship in the South Delta and connecting areas; and further migration movements due to natural seasonal influences and prevailing flow and environmental conditions. … Reclamation is not currently proposing any export restrictions, as we believe this would have little functional effect given high Delta outflow and optimal Delta smelt habitat conditions.”

In response, the US Fish and Wildlife Service stated it would review the situation and respond as soon as possible.

Acting in its role of advising the US Fish and Wildlife Service, the Smelt Working Group concluded on March 14:

“As the SWG is directed by the Biological Opinion to make OMR flow recommendations as indicated in these RPA’s, the SWG has no scope, within the adaptive range of the BiOp, to make recommendations to conserve the species. Should the Service like to suggest additional conservation tools for the SWG to evaluate (that are not indicated in the Biological Opinion), the group will meet to evaluate and make a recommendation.”


  1. The presence of spawning adult Delta smelt, their concentration in the south Delta, and their presence in salvage collections are not at all surprising.1
  2. A broad distribution of adult smelt in the Delta is also normal.
  3. There is no evidence of “high survivorship.” The catch in the Kodiak Trawl Survey (Figure 1) and other surveys remains near record lows.
  4. High Delta outflow and Old-Middle River daily average flows do not necessarily equate to low risk. Figure 2 shows that conditions in late March carry a risk of adult smelt migrating into the south Delta on flood tides.

Recommendation. Since the Smelt Working Group did not provide a recommendation, I offer the following advice:

Wet year winter losses of adult spawning smelt have always been a concern. This is the reason for the take limits. Relaxing these limits this year is unwise and unnecessary. The adult Delta smelt are now in the peak of their annual spawning run. The state and federal projects have already exported an abundant water supply this winter, and the projects should limit exports at the peak of the Delta smelt spawning season. With the State Water Project pumps shut down for repairs, a reduction of Central Valley Project exports from the present 3800 cfs to 1200 cfs could provide a real benefit. There is all the more reason to do this considering the severely depressed state of the smelt population and the possibility of some recovery in this wet year.

Figure 1. Adult Delta Smelt Catch in the Kodiak Trawl Survey in winter months of 2002-2017.

Figure 2. Late March peak flood tide flows (cfs) in the Delta. Positive downstream flood-tide flows continue in the Sacramento River and San Joaquin River channels. The Delta Cross Channel remains closed, and very strong flood-tide upstream flows thus continue into the central and south Delta. Exports have been only 3800 cfs because the State Project pumps at Clifton Court were shut down for repairs to the forebay intake. A rise in take limits would allow exports to reach 10,000 cfs or higher once forebay repairs are completed. Data source: USGS.

Yuba River Chinook Salmon – Status

A March 16, 2017 Yubanet article by South Yuba Citizens League (SYRCL) noted that the 2016 fall run of salmon for the Yuba River has dropped to the low level observed since 2007 and 2008 (Figure 1):

“The low salmon run size for the Yuba River appears to be part of another regional salmon collapse.”

Comment: the 2007-2008 Central Valley salmon collapse was attributed to several potential causes: poor ocean conditions for spawn/brood years 2004 and 2005, poor 2004-2005 Bay–Delta conditions, and lack of hatchery pen acclimation in the Bay.1 Most likely that collapse was related to drier river conditions from years 2001-2005 and critically dry years in 2007-2008, after wet conditions in years 1995-2000 resulted in high population levels. The new 2016 low is likely a consequence of the drought years 2012-2015, and specifically of poor conditions in the Yuba River.

The article also noted a high proportion of hatchery fish in the Yuba salmon run, and cited a Fishbio blog post for the following:

“It is time to decide whether we want to base our salmon production goals on sheer numbers of genetically similar hatchery fish, or on diverse, wild fish naturally supported by our local rivers.”

Comment: Since the Yuba River is the largest tributary of the lower Feather River, one would expect it to receive a portion of the wild and hatchery salmon production of the lower Feather. To define this as “straying,” given that the genetic stocks are identical, is debatable. What is unusual is that the Yuba run is made up of predominantly Feather River hatchery fish, thus indicating poor natural production from the Yuba itself, particularly in drier years. There is something about the Yuba that leads to poor natural salmon production at least during or after drought periods.

Having worked and fished on the Yuba over the past two decades, I thought I would share my insights in this post. Starting with the stock-recruitment (S-R) (recruits per spawner) relationship, I have found that, like other Central Valley salmon rivers, the Yuba has a telling and highly statistically significant S-R relationship (Figure 2) that supports the following findings:

  1. There is a basic underlying positive S-R relationship – lower spawner levels produce less recruits and visa-versa.
  2. There is a strong effect of water year conditions – wet years enhance production and dry years have generally poor production.
  3. Poor runs often come in dry years with low summer flows and high water temperatures (1988-1989, 1992, 2007-2009, 2015-2016), which may affect adult survival or the number of adults that seek the Yuba from the Feather River. Good runs occur in wet years that have higher summer flows and lower water temperatures (1982, 1996-1998). (See Figures 3 and 4.)
  4. Poor runs are also related to poor winter-spring rearing and emigrating conditions two years earlier in the Yuba and/or Bay-Delta (1989, 1992, 2009, 2015-2016). Stronger runs occurred when early rearing and emigrating conditions were good (e.g., 1986, 1995-2000).
  5. Poor runs in some years may be related to poor Feather hatchery smolt survival or poor early conditions for ocean rearing.
  6. Poor early ocean rearing conditions and lack of hatchery smolt pen acclimation in the Bay may have contributed to poor runs (e.g., 2006-2008).

In summary, there are a lot of factors that potentially affect the salmon run in the Yuba River. It is difficult to evaluate the importance of the various factors, but my bet is on two factors that stand out:

  • Higher winter-spring flows help carry young to and through the Delta, provide habitat and protection from predators, and initiate and speed migration.
  • Higher August through October flows (Figure 3): (a) attract adult salmon, (b) improve passage habitat, and (c) keep water temperatures down (Figure 4).

Figure 1. Fall-run Chinook salmon escapement estimates for Yuba River 1975-2016. Source: CDFW GrandTab.

Figure 2. Spawner – Recruit relationship for Yuba River fall run salmon. Year is recruit year escapement; for example, “16” is escapement in fall 2016 from 2013 spawn. Bold red years are critical water years. Non-bold red years are dry water years. Bold green years are above normal water years. Non-bold green years are below normal water years. Blue years are wet years. Circles represent winter-spring water year two-years earlier; for example, 08 blue circle represents winter-spring water year classification of “wet” in 2006 when the 08 spawners were rearing and emigrating from Yuba River. Yellow rectangle denotes years in which ocean conditions may have reduced escapement from poor ocean-rearing survival in prior years.

Figure 3. Lower Yuba River flow at Marysville in August-September period in years 2000-2016. Source: CDEC. Of note: lowest flows were in 2014-2016, and surprisingly in 2006.

Figure 4. Water temperature in the lower Yuba River at Marysville in 2015 and 2016. Red line is water temperature detrimental to adult salmon survival, passage, and egg viability. Yellow line denotes high stress level above 65°F. Green line is safe level below which adult survival and egg viability are good. Note: August 2015 water temperatures reached above 70°F; September-October 2015 water temperatures reached 65-70°F range. Source: Yuba River Accord M&E Field Update.

Efforts to Understand Delta Smelt Salvage

This post addresses more from the November 2016 Bay-Delta Science Conference. In this latest review I focus on:

“Part 2: Collaborative Adaptive Management Team (CAMT) Investigations: Using New Modeling Approaches to Understand Delta Smelt State Salvage Patterns at the State Water Project and Central Valley Project”.1

First, some context:

“The Collaborative Adaptive Management Team, comprised of high level managers and senior scientists, is the group that works underneath the CSAMP2 policy group. The CAMT was established [in 2013] to work with a sense of urgency to develop a robust science and adaptive management program to inform both the implementation of the current BiOps and the development of revised BiOps.”

Delta Smelt Salvage

“CAMT examined historical (1993-2015) salvage data to determine what factors affected Delta Smelt salvage at the State Water Project (SWP) and Central Valley Project (CVP) fish facilities. The objective was to determine if new approaches could be applied to the data to yield new insights about the factors that explain Delta Smelt salvage patterns within and across years.”

Comment: First, it is surprising that CAMT would apply “new” approaches and “insights” given that so much has been studied and learned about Delta smelt salvage at the south Delta pumping plants. The salvage problem had been addressed by limiting exports in winter and spring with OMR limits3 and active management by the Smelt Working Group (SWG), an effort that is both highly sophisticated and effective. The working group’s measures have markedly reduced salvage losses but have failed to curb the population decline. The measures came far too late, and managers often did not take the SWG’s advice.

More study of salvage is not going to help in learning more about the population decline. Less than ten Delta smelt were salvaged so far this winter (compared to thousands per day historically). The study of the population decline should be focusing now on freshwater inflow, Delta outflow, and spring-to-fall habitat conditions (i.e., Low Salinity Zone and water temperatures), and on the indirect effects of Delta exports. It would be far more effective to showcase the SWG’s actions and other actions required by the biological opinion and by water quality standards, It would also be more consequential for the CAMT to evaluate the consequences of weakening these standards in drought years.

“Mr. Grimaldo said that one of the initial sparring matches within the CAMT team was over conceptual models.”

Comment: The CAMT analysis and conference focused on adult Delta smelt winter salvage and the modeling effort employed to understand it. Why? Because the CAMT water contractor members do not like cutting back on exports during the infrequent winter storms in dry years, when the smelt make their spawning runs. Much of a dry year’s water supply comes in infrequent winter storms. Under the conceptual model, higher exports at such times simply draw the smelt spawners into the south Delta4 to be salvaged (killed at fish screens or lost in forebay). When the spawn is in the south Delta, it also makes the annual production of larvae more vulnerable to unmonitored/unmeasured entrainment into the export pumps later in spring. The US Fish and Wildlife’s Delta Smelt Biological Opinion addresses these risks by limiting winter-spring exports. There is no doubt that until these risks are further reduced, there will be no recovery of the Delta smelt population (or other listed Delta fish). Furthermore, until protective actions are extended to Delta outflow, salinity, and water temperatures, there will be no recovery, and the conflict with water supply will remain unresolved and a perpetual problem.

“Grimaldo acknowledged that the Fall Midwater Trawl nowadays is pretty lousy for sampling Delta smelt. “We get very few,” he said. “So this problem is even worse as now we don’t even have a gear, so we don’t even have an idea what the size is coming into December.”

Comment: There is nothing wrong with the Fall Midwater Trawl Survey. It captures few smelt because there are few left. All the surveys support this conclusion (see chart below). We are doing just fine in data gathering with the Smelt Larval Survey, the 20-mm Survey, the Summer Townet Survey, the Fall Midwater Survey, and the Fish Salvage Survey.

The relationship (log-log) between the fall midwater trawl index and the subsequent summer townet survey index (year noted) is remarkably significant, especially when water-year type is taken into account. Red years are dry/critical. Green years are below/above normal. Blue years are wet.

“Grimaldo suggested that a Kodiak trawl should start in September. “We know that it catches fish better than the fall midwater trawl. I think folks just have to make the leap. I think folks are used to the Fall Midwater Trawl being this 40 year plus monitoring device, but maybe we need to switch things up, because we know from other work that Ken Newman and Randy Baxter are doing that this Kodiak is a better gear for sampling Delta smelt, so why not go for it. This could potentially allow for salvage losses to be evaluated in the context of a recruit responder model,” he said. “At least you could have an idea going into the salvage season what your salvage actually means.”

Comment: The context that matters is that the indices and salvage are near zero and have been for several years. Yes, the highly effective Kodiak trawl would be more effective at near zero population. Do we really want to manage the population down at zero, or do we want to smelt to recover?

Final point: It is sad that we have to resort to court-directed science in the form of CSAMP/CAMT to resolve the perpetual conflict between water management and the Delta ecosystem. All the effort will be focused on how the ten smelt salvaged this year could have been reduced to five.

Can rice fields help save endangered salmon?

A recent article in the LA Times asked: can rice fields help endangered salmon in the Central Valley? Because that article really did not answer the question, I thought I would try in this post. The answer is: absolutely.

A significant portion of the endangered winter-run and spring-run salmon populations are now made up of hatchery fish. Hatchery fish are important in keeping the populations from falling further toward extinction and in helping toward recovery. To make the hatchery tool in the tool-box of recovery more effective, it is essential that a greater percentage of hatchery eggs become smolts that reach the ocean. Studies show that hatchery smolts released at or near hatcheries have a very poor survival rate to the Golden Gate. Trucking the hatchery smolts to the Bay increases survival, but results in significant straying to other Valley rivers.

Rice-field-reared salmon. Source: UC Davis photo

One way to increase smolt production and survival is to rear a portion of the newly hatched fry in Valley floodplain rice fields closer to the Bay. There have been plenty of experiments that show fall-run hatchery fry do well in terms of growth and survival in rice fields. The next step is putting that knowledge into management action. At a minimum, rearing a portion of newly hatched fry from hatcheries in natural floodplains is more “natural” than rearing them in hatchery raceways.

Winter-Run Salmon: Winter-run fry from the Livingston Stone federal hatchery could rear in the rice fields of the upper Yolo Bypass during late fall and early winter. Conditions would be ideal for growth and survival. Even in drought years, water would be available from the Colusa Basin Drain, whose water source is primarily the upper Sacramento River. As proven last year, managers could explicitly divert water for this purpose from near Red Bluff on the Sacramento River, through the Colusa Basin to the upper Yolo Bypass rice fields, and finally to the Tule Canal. This would facilitate emigration of the smolts produced to the Bay. The planned Fremont Weir “fix” will provide Sacramento River water directly to the Yolo Bypass within several years. The alteration of Fremont Weir will also provide passage back to the Sacramento River for any adult winter-run that are attracted to Yolo Bypass flows.

Spring-Run Salmon: Spring-run fry from the Feather River state hatchery could rear in rice fields in the lower Sutter Bypass adjacent to the lower Feather River. Rearing would occur in winter, when conditions would be ideal. A late winter flow pulse could facilitate the emigration of these fish (as well as wild fish) out of the Feather River to and through the Delta, and to the Bay and ocean.

What ifs:

  • What about predators? Rice-field-reared winter-run smolts will have 100 miles less migration through the upper Sacramento River gauntlet of predators. Feather River rice-field smolts will be able to pass almost directly into the lower Sacramento River, thereby avoiding many miles of predator habitat in the lower Feather River. Yolo Bypass winter-run smolts would pass through 40 miles of the Tule Canal to reach Cache Slough in the Delta. Added flow and colder mid-winter water temperatures should minimize this real risk. Remember also that rice field habitat is seasonal. Bass and other species that dine on juvenile salmon don’t establish themselves in rice fields like they do in waters that are inundated year-round.
  • How will the progress of these fish be measured? Like all other hatchery fish, these fish should all be coded-wire tagged, and a small portion should be radio-tagged, prior to release.
  • What about straying? Rearing in the appropriate source water should help to minimize straying. Providing flow pulses during emigration will help in imprinting. Imprinting newly hatched fry at the hatcheries will also help.
  • What about contribution to the population, especially given potentially low Delta survival in dry years? If necessary, the rice-field-produced smolts could be readily transported by barge from nearby Verona on the Sacramento River. They could also be released directly to the nearby Sacramento River or trucked to the Bay. In any event, the rice-field-reared smolts should reach the ocean about a month earlier and at a larger size than their hatchery-reared counterparts, which should lead to a marked survival advantage.
  • What if such a program is too successful? This would be a great problem to have, for once. Too many hatchery fish could jeopardize the genetic viability of the population. If that becomes a problem, such a program (or the overall hatchery program) could be scaled back. But until we reach that day, floodplain rearing of hatchery fry is a more natural and more effective tool for the recovery toolbox than more conventional hatchery practices.
  • What about landowners? Many rice field land owners and managers are fully supportive and are committed to implementing such a program.
  • What about stakeholders and resource agencies? Such a program has yet to be implemented on a large scale to test if it can meet its objectives. There is a natural reluctance on the part of agencies to commit endangered salmon resources to something unproven like this. Pilot studies to date have proven the concept is viable. An appropriate next step is a large-scale contribution study involving several hundred thousand or more fry, in sufficient number to assess potential contribution to the population.

Science Perspectives – 2016

The Bay-Delta Science Conference held this past November focused on the topic of “Science for Solutions: Linking Data and Decisions”. There were a diversity of subjects and presentations on the topic. A special series of papers previewed the conference presentations in the San Francisco Estuary and Watershed Science (UC Davis). The conference presentations and journal articles were a lot to take in.

My take on the conference and associated journal articles is that they represent a continuation of a decades-long attempt to avoid and direct focus away from the root cause of the Bay-Delta ecosystem’s greatest problems: high Delta exports, low river flows to the Delta, and low Delta outflows to the Bay under past and present water management. Simply put, there was a lot of the “same-old, same-old” mix of perspectives (excuses), with some new and interesting science.

A previous post covered the conference paper on Delta smelt. Another covered introductory presentations. In this post I focus on one presentation and paper entitled Perspectives on Bay-Delta Science and Policy, a summary of the conference prepared by its sponsor’s (the Delta Stewardship Council) Independent Science Board.


“Perspectives” focuses on seven themes the Independent Science Board has grown to accept as the causes of the Bay-Delta problems (Figure 1):

  1. Nutrients – Changes in and lack of nutrients are now considered important.
  2. Contaminants – Delta waters are now considered contaminated.
  3. Food Webs – Much less able to support fish than in the past.
  4. Multiple Stressors – Multiple stressors work together to cause the decline in Delta native fishes.
  5. Storms and Droughts Extremes – Extremes in drought and floods wreck havoc on water management.
  6. Landscape Ecology – Restoration has not been pursued on a landscape scale.
  7. Dire Straits of Endangered Species – Regime shifts and climate change have contributed to accelerated spiraling declines in native fishes.

Even if the underlying science on the subjects (factors) is valid, the arguments that relate these factors to the Bay-Delta ecosystem decline are not. At most, these factors are secondary actors in the overall process driven primarily by water management, Central Valley and Bay-Delta water quality standards, and endangered fish “protections in biological opinions.

The focus on these perspectives represents an overall intent to misinform and misdirect science and management away from real causes and effects, and from effective solutions to the Delta’s problems. Some topic examples:

  • “In the past we considered nutrients to be relatively unimportant in Delta productivity.” Untrue. The loss of nutrients that went along with water quality improvement over the past half century were always a concern. Sewage treatment upgrades were considered a factor in declines in Delta fish production. Aerial fertilization of the Delta was considered at least two decades ago.
  • “The low salinity zone, once a food-rich region of the Delta, now provides little food for native fish.” This statement is untrue. The LSZ remains the key rearing area of the Central Valley for smelt, salmon, sturgeon, and splittail, because it has the highest concentrations of “food” in the Bay-Delta Estuary.
  • “Aquatic food webs no longer sustain native fishes.” Untrue. Native fish are sustained if given a chance. Smelt and salmon were nearly recovered in 2000 after six wet years and massive recovery efforts and new protections. The protections simply failed to carry over into dry sequences 01-05, 07-10, and 12-16. Poor food, growth, and survival are caused by man-made drought conditions, and lack of protections of the pelagic food web of the Bay-Delta in drier years.
  • “There are few instances in which a single stressor can be identified as the primary cause of any species’ declines.” Untrue. River flow and exports are often the single most important factors in single events, such as winter-run salmon year-class failures below Shasta.
  • “Effective conservation requires a holistic approach.” Yes, one that does not take most of the fresh water from the rivers, Delta, and Bay.
  • “The aquatic ecosystem has gone through a regime shift that cannot be reversed.” Untrue. Taking most of the water out of the estuary from late winter through fall every year keeps the aquatic ecosystem in a semi-permanent drought, broken only by wet water years when large amounts of unregulated water escape capture by water managers. The patterns of the 2010-2011 water years show that negative patterns can be reversed.
  • “The problems have been caused by invasive clam and aquatic plants, and other non-native animals of the Bay-Delta foodweb.” Untrue. These are for the most part secondary responses to the real cause: greater exports and low river flows.
  • “More frequent and extreme storms and droughts will occur.” Four of last five, seven of last ten, and ten of last sixteen years have been part of drought sequences. From 1987 through 1996, seven of ten years were drought years. Water year 2017, though extreme, is not unlike previous very wet years.
  • “Habitat restoration has cascading effects.” In truth, restoration has as yet been minimal, with minimal evidence that it contributes substantial beneficial effects.
  • “The ecological regime shift and climate change are accelerating decline of native species.” While climate change certainly is not helping, the declines of native species are for the most part avoidable by reducing demands on water. The most important “regime shifts” of the last several decades have been shifts in water management strategies.


The Independent Science Board’s editorial board extracted the following forward-thinking actions from their 2016 Perspectives paper:

  1. Incorporate long-range (50 year) thinking into Delta science and management. Acknowledge the accelerating rates of change ahead, and the inability to return to past conditions, in evaluating and planning feasible options for the future. Long-term planning is generally a good idea, but this formulation ignores current reality and the need to (1) return to past levels of protection, and (2) be wary of water management strategies that would further undermine the Bay-Delta ecosystem.
  2. Incorporate more exploratory and forward-looking science into government science programs at all levels, including science not tied to any current policy or crisis. Start planning now for about 15% of the overall Delta science budget to transition into more forward-thinking science. More science is not the answer. More science is more smoke.
  3. Widen science career paths in state agencies so that scientists are not forced to abandon science to advance their careers. More scientists are needed in management to apply the science that is already available.
  4. Plan for variability and extremes in the decades ahead, as well as long-term change. Bolster the ecosystem’s capacity to absorb both drought and deluge by continuing to reduce the state’s demand for water supply from the Delta, as required by the Delta Reform Act of 2009. Replenish Central Valley groundwater reservoirs and promote agricultural practices more resilient to drought. Adjust water management practices to accommodate less predictable sources of supply and more variable flows. Sound advice.
  5. Adapt management practices to take advantage of any ecological, recreational, and economic values to be gained. Yes, take advantage of low cost, high benefit practices.
  6. Begin the scientific and societal groundwork needed to seriously explore alternatives to conservation in place for endangered species. Continue all reasonable efforts to provide for them, including reducing water demand on the Delta, but recognize that the time has come to develop the science and policy foundations for more radical approaches, including assisted relocation, assisted evolution, and cryopreservation. There is also a need to enhance and build conservation hatcheries. But most of all, we need to protect and enhance the resources we have left.
  7. Invest now to develop models of the Delta system, analogous to global climate models, that more fully integrate physical, ecological, and social sciences. Use these models to forecast likely outcomes from changing climate and other external forces acting on the Delta, as well as likely effects of various management policies. Math models of complex ecosystem function are unnecessary – simpler conceptual and statistical (data) models are more realistic and better management tools.
  8. Weave “Delta as an Evolving Place” into all science, planning and management programs. Stop allowing further “evolving” and start de-volving where reasonable. The Bay-Delta is not really evolving; it is just ever-increasingly being disturbed.

Rethinking the above perspectives and actions would be a reasonable first step toward a more progressive strategy for the Delta Science Board.

Figure 1. Perspectives on Bay-Delta Science and Policy. (Independent Science Board)