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.

New Winter Run Salmon Science

The November 2016 Science Conference had a series of presentations on the latest Sacramento River winter run Chinook (SRWRC) salmon science. Some conclusions from the presentations with my comments follow:

  1. “Recent modeling advances reviewed here give deeper insight into the interacting causes of SRWRC’s vulnerability to extinction and add further support to the need for the high-priority actions identified in the SRWRC recovery plan.” Models show the continuing risk posed by the existence of just one spawning run, downstream of Shasta. The NMFS Recovery Plan prescribes a Battle Creek population and an above-Shasta population. Progress toward both has been slow.
  2. “Winter run chinook salmon have gone through several major droughts in 1977-76, 1988-92, and 2013-2016 where environmental conditions were extremely poor. With each new drought, new insights are realized and additional levels of management actions are taken, or proposed using an ever-increasing science based knowledge base.” Over the years, there have been major actions to improve the condition of winter run salmon downstream of Shasta: (1) a temperature control tower at Shasta Dam, (2) removal of the Red Bluff Diversion Dam, (3) screening of major Sacramento River water diversions, (4) the addition of a winter run hatchery, and (5) restrictions on winter exports from the Delta. All of these actions have certainly helped. However, the continuing drawdown of Shasta Reservoir during dry years leads to loss of the cold-water pool and to low water releases. These conditions undermine spawning, egg incubation, rearing, emigration survival, and thus limit subsequent adult spawner returns. Better water management below Shasta is essential for winter run salmon recovery.
  3. “Lessons from the ongoing drought have highlighted the potential benefits of improved forecasting capabilities of temperature dynamics above, within, and below Shasta Reservoir for better management of cold-water resources.” The lesson learned is that agencies cannot stretch water deliveries to the limit without jeopardizing short- and long-term water supplies and salmon habitat conditions. Poor forecasting tools have not helped. Improved monitoring has helped. But in the end, it has been risk-taking that has undermined the winter run salmon population. Chief among the risks have been flow and temperature regimes at or worse than the known tolerance of the salmon.
  4. “We conclude that descriptive models of thermal tolerance can drastically underestimate species responses to climate change and that simple mechanistic models can explain substantial variation in the thermal tolerance of species.” In other words, reliance on the tolerances of eggs and embryo salmon as observed in the laboratory fails to take into account nuances in the river habitats of salmon. Such reliance underestimates the effects of management actions. “New science” will lead to more conservative prescriptions for protecting salmon in the future, with corresponding impacts to water supply.
  5. “Infection by the myxozoan parasites, Ceratonova (previously Ceratomyxa) shasta and Parvicapsula minibicornis, has been observed in all Sacramento River adult runs, and juvenile fall and winter-run Chinook. In 2014, infections were lethal for over half of the spring out-migrants sampled from the lower river. In fall of 2015, sentinel juvenile salmon, held above Red Bluff diversion dam, incurred a high prevalence of severe infection.” Another consequence of very low river flows in fall and winter of drought years is the prevalence of disease, which reduces survival of rearing and out-migrating salmon. This may be the most significant new science, because it could lead to more protective water quality standards in the Sacramento River downstream of Shasta.
  6. “For salmon in a natural system increased river flow from rainstorms is the environmental cue that causes synchronous mass out-migration of juveniles.” When there are natural flow pulses in the Sacramento River system, there is the obvious need to mimic those pulses with corresponding flow releases from Shasta and Keswick dams. Otherwise, the 10-mile tailwater immediately downstream of Keswick will not have a stimulus flow to match that of un-dammed tributaries further downstream (e.g., Battle Creek).1
  7. “Non-natal habitats that could be identified were the Mt. Lassen tributaries (used by 56%, 19%, and 15% of all non-natal rearing fish from escapement years 2007-2009), the American River (22%, 40%, and 38%), and the Delta (11%, 36%, and 32%). The time period spent within the non-natal habitats ranged from approximately 2 to 16 weeks. These results suggest the extent of WRCS juvenile rearing habitat is likely under sampled and that non-natal habitats are potentially contributing significantly to the WRCS spawning population. Thus, we believe protecting and restoring,non-natal rearing habitats can play an important role in recovering the winter-run Chinook salmon population.” It has been long known that Chinook salmon use non-natal tributaries in the Central Valley for rearing. What is new is the understanding of the extent of this life history pattern. Winter run are known to start their emigration in the fall and spend much of the winter in the lower River and upper estuary before migrating to the Bay and ocean in late winter. The 2 to 16 weeks spent in lower tributaries and other floodplain habitats can double the weight of smolts and greatly increase their survival potential upon reaching the ocean. This research is likely to result in more emphasis on habitat restoration in the lower tributaries.
  8. “Ultimately, the productivity of the shelf ecosystem is tied to the survival and growth of the out-migrating salmon…. Larger out-migrating individuals, when faced with an unproductive ecosystem, have a greater likelihood of survival.” Survival of young salmon is tied to freshwater conditions that promote growth: habitat. food availability, water temperature, and flows.

San Joaquin Salmon Population Status – End of 2016

Recently, I wrote about the fall Chinook salmon runs on the San Joaquin River and its three major tributaries over the past six years.  Salmon counts in San Joaquin tributaries showed an increase in returning adults in 2012-2015 compared to the devastating returns in 2007-2009.  This increase occurred despite the five-year (2012-2016) drought in the San Joaquin watershed.  The number of spawners in 2012-2015 was still well below the returns in the eighties and nineties that corresponded to wet water year sequences.  See Figure 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 years with dry winter-springs or dry falls.  That relationship overwhelms the background relationship between spawners and recruits three years later.

  1. Recruitment is significantly depressed in drier years compared to wetter years. The major contributing factor is likely poor survival in winter-spring of juveniles in their first year.
  2. Recruitment is severely depressed for year classes rearing in critical years and returning as adults two years later in critical years (e.g., 88, 89).
  3. Recruitment can be depressed for year classes with good winter-spring juvenile rearing conditions but poor conditions when adults return (e.g., 05, 06).
  4. Recruitment can be enhanced for year classes with poor winter-spring young rearing conditions but very good fall conditions for adults returning (e.g., 81).
  5. Recruitment was enhanced in recent years likely as a consequence of increased flow requirements since 2009 (e.g., 09-13).
  6. There is an underlying positive spawner/recruit relationship, but it is overwhelmed by the effect on recruitment of flow-related habitat conditions.
  7. Poor ocean conditions in 2005-2006 likely contributed to poor recruitment.

Figure 1. Chinook salmon runs in the San Joaquin River as comprised by its three spawning tributaries from 1975-2015. Data source: CDFW.

Figure 2. Recruits per spawners relationship ((log10X)-2) for San Joaquin River fall run Chinook salmon 1976-2015. The year shown is the year that the salmon were rearing as juveniles in the rivers in their first year of life. (For example: year 13 represents the progeny of the fall 2012 spawn; these juveniles in 2013 would have spawned as 3-year-old adults in 2015). Red years are critical and dry water years. Blue years are wet water years. Green years are normal water years. Red circles represent years when fall conditions during spawning would have reduced recruitment (for example: year 13 red circle indicates poor fall conditions during the fall of 2015). Blue circles represent years when fall conditions were good when recruits returned. (For example: year 81 has blue circle because 1983 fall conditions were good/wet year). Note that year 14 is as yet unavailable for inclusion in the dataset because run counts for fall 2016 are not yet available.

Annual Runs in the Back Yard

Last week, the annual arrival of cedar waxwings hit my back yard near Sacramento. Each January, these magnificent birds fill my small back yard by the hundreds to feast for several days on the fermented fruit of three tall grape trees. The birds eat nearly every grape, likely a ton of fruit hanging from the branches. In several days the birds are gone, not to return for another year. I often wonder how important my little backyard piece of habitat is for this population of Cedar Waxwings, and how much of their winter energy comes from this small crop of fruit.

The birds remind me of another annual backyard run, the Cook Inlet Coho and Chinook salmon near Anchorage, Alaska, where I lived for three years in the mid-1980s. A large run of Coho showed up right on time each year at the end of summer in a creek that was literally in my back yard. Only kids were allowed to fish the city’s creeks for salmon, so I taught the neighborhood’s boys, including my 12-year-old son, how to catch and release the Coho. For a week or two, they could catch five or so bright ten-pounders in an hour or two a day. Me, I canoed down a tidal creek on the Kenai Peninsula side of the inlet and camp for a weekend to fish the fresh Coho run entering from the Inlet. I built a blind right on the creek within sight of the inlet. I could see the white backs of dozens of Beluga whales herding and feeding on the incoming salmon just a few dozen yards off the creek mouth. At night, the Coho approached the light of my Coleman lantern, even allowing a brief pet or two on my part, while maintaining steady and wary eye contact.

In the spring (late May), I often hitched a plane ride across the inlet (10 minutes and $40) to fish the spring Chinook run for a weekend of 24-hour daylight. At low tide, the small rivers were over 30-ft below the tule-lined channel. At high tide, the channel filled to the tules, along with seemingly bank-to-bank 30-lb spring-run salmon that obligingly hit any lure I put in front of them. This annual rush of spring Chinook lasted for a week or two before the fish moved upstream to await their late summer spawn.

Today, thirty years later, things are not so good. After 30 years of increasingly intense subsistence, personal use,1 sport, and commercial fishing pressure, and most importantly severe ecological drought, the salmon runs have sharply declined. No doubt global warming has hit Alaska worse than other parts of North America, with high temperatures and low precipitation.2

Many of the streams are now closed to fishing. Where open, the annual bag limit of Chinook is only one fish per year. The Cook Inlet Beluga that once numbered in the thousands are down to several hundred and were listed as endangered in 2008. This decline occurred despite the fact that much of the habitat remains virtually pristine and untouched by man, with little influence of hatcheries. Global warming, overfishing, natural cycles, or ocean conditions: no one knows the cause for sure. Regardless, Alaska’s fish agencies must now manage its fisheries very conservatively with intensive adaptive management science. If you asked these agencies, they would say they had already been doing that for decades. They would also admit they learned a hard lesson. For more on their situation see:
http://www.adfg.alaska.gov/index.cfm?adfg=wildlifenews.view_article&articles_id=516 .

  1. Each state resident family could use a gillnet in the Inlet to catch 50 salmon per year for “personal use”.
  2. https://nccwsc.usgs.gov/content/ecological-drought-alaska

PG&E Withdraws License Application on Butte Creek: Future of Spring-Run Salmon Uncertain

By Chris Shutes (CSPA) and Dave Steindorf (American Whitewater)

In a surprise move, PG&E announced on February 2, 2017 that it was withdrawing its application to relicense the DeSabla – Centerville Hydroelectric Project on Butte Creek and the West Branch Feather River.  The reach of Butte Creek affected by the Project is home to the only remaining viable population of spring-run Chinook salmon in California’s Central Valley.

Spring-run salmon in Butte Creek have seen a resurgence over the last twenty years.  A substantial part of this was due to investments and improvements downstream of the Project. In addition, since 2003, PG&E and state and federal resource agencies have greatly improved the management of the Project for the fish.

From 2004 to 2009, PG&E went through a formal relicensing process with the Federal Energy Regulatory Commission (FERC) to relicense the Project.  In 2016, the State Water Board issued a Water Quality Certification needed for a new license.  A new license from FERC was widely expected in 2017.

In a DeSabla – Centerville fact sheet and map that PG&E distributed with its announcement, PG&E describes the project as follows:

The Project diverts a portion of the natural flow of water from Butte Creek and West Branch of the Feather River (WBFR) into canals that carry the water for use in hydroelectric powerhouses. Once water is run through the powerhouses it is ultimately released to Butte Creek. During the summer, the natural flow of the WBFR is augmented by water releases from Round Valley and Philbrook reservoirs. Project diversions have provided additional flow to Butte Creek for more than 100 years. One of the beneficiaries of this additional flow has been the aquatic community in Butte Creek, including Central Valley spring-run Chinook salmon.

While it is true that water from the Project augmented flows below Centerville Powerhouse for 100 years, it is only since 1980 that the Project benefited fish in the eight miles of Butte Creek between DeSabla Powerhouse and Centerville (see map).  The 2016 Water Quality Certification requires all the Butte Creek water and the imported water to remain in Butte Creek once it exits DeSabla Powerhouse.

The DeSabla – Centerville Project facilities are built around infrastructure that dates to 1900 and in some cases before.  Commissioned in 1900, Centerville Powerhouse has been offline since 2011, and ran only partially for the five years previous to that.  To function at all, it would need a complete rebuild.  The estimated cost to rebuild was $39 Million in the mid-1990’s; it is almost certainly now double that, or more.  DeSabla Powerhouse, nine miles upstream of Centerville, is relatively modern and in good condition, but the small reservoir that feeds it allows water to heat up too much passing through.

In California’s modern energy market, the capability to regulate the grid gives hydropower its greatest value.  But unlike many other hydropower projects, powerhouses in the DeSabla – Centerville Project run at a constant rate, day and night, regardless of when power demand is high or low.  They also have no ability to help regulate the power grid, especially to respond to short-term changes in supply from intermittent renewable sources like wind and solar.

The real value of the Project is the water it imports from the West Branch Feather River to Butte Creek: value for the fish and value for the farms that use the water further downstream.  The fish can’t pay for this service; the farms have never been asked to pay and never have.

PG&E’s decision not to relicense the Project does not lead to a path that is simple.  In the next few months, moving into the next few years, PG&E will need to establish a stakeholder engagement process to help determine the Project’s long-term disposition.  PG&E will need to engage resource agencies, downstream water rights holders, interested NGO’s, and local residents.  The DeSabla – Centerville Project has been part of the community for over a century.  Its resource values are enormous.  The water that it supplies downstream is essential to the irrigation of thousands of acres of crops.

On September 19, 2015, PG&E bought an advertisement on the editorial page of the San Francisco Chronicle entitled:  “Of Bees, Birds and Chillin’ Chinook: All in a Sustainable Day at PG&E.”  Mr. Tony Earley, CEO of PG&E at the time, started the ad by extolling PG&E’s work to keep salmon in Butte Creek cool.  His major theme stated: “The days are long past when energy companies could afford to think of their mission as separate from conservation, sustainability and good management of our natural resources.  Our view must be for the long term.  That’s why we live our commitment to conservation through a number of programs.”

We look forward to the opportunity to help PG&E maintain this well-stated goal.

Longfin Smelt – January 2017 Larval Survey

In a recent post on the status of the state-listed longfin smelt, I remarked on the dire straits of the population in the San Francisco Bay Estuary.  I noted that the first measure of a population collapse would be the lack of population response in wet year 2017 as determined by the larval longfin smelt catch in the January 2017 Smelt Larval Survey.  The January 2017 survey results are now in and indicate very low catch (15) relative to the first eight years of the survey.  Additional larval surveys in February and March and the spring 20-mm Survey will likely confirm these results.  The low larval count reflects the lack of adult spawners in the population.  Most of the winter 2017 spawners came from the winter 2015 brood.  The question remains whether the population can rebound under such low recruitment of juveniles into the population and whether juvenile survival (recruit per spawner) can increase under 2017’s favorable wet year conditions.

Catch of longfin smelt in January Smelt Larval Survey 2009 to 2017. Data Source: http://www.dfg.ca.gov/delta/data/sls/CPUE_Map.asp .

Catch of longfin smelt in January Smelt Larval Survey 2009 to 2017. Data Source: http://www.dfg.ca.gov/delta/data/sls/CPUE_Map.asp .

More on Delta Smelt Tidal Surfing

The last post about risk to Delta smelt was on January 9. Adult smelt migrate into the Delta from the Bay in winter to spawn. They take advantage of the flood tide to move upstream. However, with flood flows as high as 100,000 cfs entering the north Delta from the Sacramento River, the Yolo Bypass, and Georgiana Slough in mid- to late January 2017, there are no flood tides to ride into the north Delta spawning areas.

The only option for the adult smelt is thus to ride the incoming tide up the San Joaquin River into the central and south Delta (Figure 1). South Delta export pumping is currently at 14,000 cfs, near maximum capacity, using four rarely used auxiliary pumps. This pumping increases the pull of the incoming tide, reducing the effect of the inflow from the San Joaquin, Calaveras, Mokelumne, and Cosumnes rivers. While Delta inflow from these rivers is relatively high (Figures 2-5), it does not offset the influence of the incoming tide as does the inflow from the Sacramento.

Net tidal flows in lower Old and Middle Rivers (OMR flows) remain at the allowed limit of -5000 cfs, consistent with the smelt Biological Opinion. Several adult Delta smelt were salvaged at the export facilities in mid-January. 1 This scenario is considered a “high risk” to Delta smelt by the Smelt Working Group, because of the continuing risk that the pumps will draw or attract adult smelt into the central Delta and subsequently into the south Delta.

Under lower San Joaquin River flows, the maximum allowed export pumping is 11,400 cfs. High San Joaquin River inflow allows exports of 14,000 cfs that do not generate OMR flows more negative than -5000 cfs. The theoretical benefit of high San Joaquin River flows is that it should keep flow into the central and south Delta moving westward. But a large portion of that inflow is diverted south into the Head of Old River toward the pumping plants (Figure 6).

Figure 1. Approximate flood tide flow in cubic feet per second in mid to late January 2016. Blue arrows represent high Sacramento River, San Joaquin River and Mokelumne River flows (during flood tides). Red arrows depict negative flows of incoming tides. Note the south Delta incoming tide of -20,000 cfs would be less if not for the 14,000 cfs export rate at the south Delta pumping plants.

Figure 1. Approximate flood tide flow in cubic feet per second in mid to late January 2017. Blue arrows represent high Sacramento River, San Joaquin River and Mokelumne River flows (during flood tides). Red arrows depict negative flows of incoming tides. Note the south Delta incoming tide of -20,000 cfs would be less if not for the 14,000 cfs export rate at the south Delta pumping plants.

Figure 2. San Joaquin River flow at Mossdale at the head of the Delta upstream of Stockton and the Head of Old River. Note that on Jan 6 when flow reached about 6,000 cfs, the tidal signal dissipated when flow overcame the tidal forces.

Figure 2. San Joaquin River flow at Mossdale at the head of the Delta upstream of Stockton and the Head of Old River. Note that on Jan 6 when flow reached about 6,000 cfs, the tidal signal dissipated when flow overcame the tidal forces.

Figure 3: Flow from the Calaveras River, upstream of the Delta. The Calaveras enters the Delta at Stockton.

Figure 3: Flow from the Calaveras River, upstream of the Delta. The Calaveras enters the Delta at Stockton.

Figure 4. Release from Camanche Dam to the Mokelumne River. CDEC does not show flow values for the Mokelumne at gages further downstream. The Mokelumne enters the Delta near Jersey Point.

Figure 4. Release from Camanche Dam to the Mokelumne River. CDEC does not show flow values for the Mokelumne at gages further downstream. The Mokelumne enters the Delta near Jersey Point.

Figure 5. Cosumnes River flow well upstream of the Delta. Much of the high flow peaks enters the river’s connected floodplain, roughly between Lodi and Elk Grove, and does not flow immediately to the Delta. Flows in the Cosumnes enter the Mokelumne before passing into the Delta

Figure 5. Cosumnes River flow well upstream of the Delta. Much of the high flow peaks enters the river’s connected floodplain, roughly between Lodi and Elk Grove, and does not flow immediately to the Delta. Flows in the Cosumnes enter the Mokelumne before passing into the Delta

 Figure 6. Flow entering the entrance to Old River from the San Joaquin River near Stockton.


Figure 6. Flow entering the entrance to Old River from the San Joaquin River near Stockton.

  1. https://www.usbr.gov/mp/cvo/vungvari/dsmeltsplitdly.pdf Note: website has changed to this new site.

More on Splittail Status

Recently, I summarized survey information from the Bay-Delta on Sacramento splittail that depicted a potentially grim picture of the future of this special status species.  In that post, I did not include trawl survey info from Suisun Marsh Fish Study collected annually by UC Davis (Figure 1), which indicates a core population of adult splittail still present in Suisun Marsh.  Other core populations exist in San Pablo Bay (Petaluma and Napa Rivers).  Peter Moyle and Teejay O’Rear (UC Davis, personal communications) believe the Marsh core population is sufficiently strong and resistant to extinction.

Looking at Figure 1, the Suisun Marsh population survived the 1987-1992 drought, building in numbers with strong recruitment (ages 0 and 1) in the wet years of 1995-2000.  Recruitment declined during the 2007-2009 drought, but there was strong recruitment in the wetter 2010 and 2011 water years.  Recruitment declined in the 2012-2014 drought years, but remains substantially higher than at the end of the 1987-1992 drought.  Teejay O’Rear states the population has remained strong through 2015 and 2016, with some recruitment in the wetter 2016, and likely strong recruitment in the spring of 2017, presuming it stays wet.

Figure 1. Catch-per-unit-effort of Sacramento splittail in Suisun Marsh 1980-2014 by age group. (Source: Teejay O’Rear, UC Davis)

Figure 1. Catch-per-unit-effort of Sacramento splittail in Suisun Marsh 1980-2014 by age group. (Source: Teejay O’Rear, UC Davis)

Restoring Side Channels in the Upper Sacramento River

In a prior blog entry on this site, the importance of restoring juvenile salmon rearing habitats in the upper main stem Sacramento River downstream of Keswick Dam was described:   http://calsport.org/fisheriesblog/?s=rearing+habitat.  The main river channel is actually a harsh environment for young salmon upon emergence from the river gravels after hatching.  The weak-swimming fry are immediately exposed to very high water velocities and most of the riverbed lacks structure to provide those fish with velocity and predator refugia.  One hypothesis, albeit very difficult to prove, is that insufficient rearing habitats in the upper river may be a significant limiting factor for the salmon runs, particularly for the endangered winter-run Chinook.

Although the notion of increasing the quantity and quality of rearing habitats in the main stem Sacramento River has been discussed for decades, meaningful on-the-ground restoration actions have been lacking.  That circumstance is changing.  A management action now being pursued is the restoration of side channels that have lost ecological functions for salmon rearing, primarily because of diminished or total lack of hydraulic connectivity with the main river channel.   Many of the historical side channels have become plugged, stagnant, and choked with overgrown vegetation; excellent frog habitat, but not for salmon.

A major endeavor to reopen some side channels, probably the most complex in modern times, was recently completed on the upper Sacramento River in Redding, California (Figure 1).  Termed the North Cypress Street Project, multiple agencies and stakeholders successfully planned, initiated, and completed this action in 2016.  Finishing touches on the project were completed just prior to the new year.  Funding was provided by the Central Valley Project Improvement Act Anadromous Fish Restoration Program.  According to the Western Shasta Resource Conservation District which provided oversight for the entire effort, restoration of these side channels will provide rearing habitats for winter-run and fall/late-fall-run Chinook (Figure 2) through the provision of optimal flows, refuge from predators, and increased food sources.  The habitats will be particularly important for winter-run Chinook because nearly the entire population now spawns upstream of the site.

Figure 1.  Location of the North Cypress Street side-channel project to restore juvenile salmon rearing habitats.  The Painter’s Riffle project is located just upstream of Cypress Street which was previously described in this blog:  http://calsport.org/fisheriesblog/?s=painter.

Figure 1. Location of the North Cypress Street side-channel project to restore juvenile salmon rearing habitats. The Painter’s Riffle project is located just upstream of Cypress Street which was previously described in this blog: http://calsport.org/fisheriesblog/?s=painter.

Figure 2.  Rearing juvenile Chinook.  California Department of Fish and Wildlife photograph.

Figure 2. Rearing juvenile Chinook. California Department of Fish and Wildlife photograph.

The completed restoration provides up to 1.48 acres of new side-channel rearing habitats at the minimum Keswick Dam release of 3,250 cfs (Figure 3).  The restoration included installation of numerous large woody debris structures to increase the habitat complexity for young Chinook.  Video footage of the project by John Hannon is provided at:  Side Channel Projects

More such actions are planned for implementation on the upper Sacramento River in 2017 and years beyond.

Figure 3.  Post-construction schematic of the North Cypress side-channel project.  Restored side channels are depicted by blue lines (courtesy of the Western Shasta Resource Conservation District).  Sacramento River flow is from the upper right to the lower left in the photograph.

Figure 3. Post-construction schematic of the North Cypress side-channel project. Restored side channels are depicted by blue lines (courtesy of the Western Shasta Resource Conservation District). Sacramento River flow is from the upper right to the lower left in the photograph.

More on Delta Science

More Delta ScienceI have written often on Delta science and what has been or could be learned from science to support water management.  Yet another biennial Delta science conference, the 9th, was held this past November.  This year’s conference theme was: “Science for Solutions:  Linking Data and Decisions.”  Another year has passed, and more has been studied and learned.  More dots have joined the dozens of previous dots in data charts from annual surveys of Delta organisms and habitat conditions.  More dots lament the loss of water and habitat.  The huge Delta Science Program has progressed yet another year.

Opening Talk

In Phil Isenberg’s opening talk, “A Guide for the Perplexed”, the former legislator and former chair of the Delta Stewardship Council suggested that scientists learn to smile more.  He asked: “Why should science be involved in policy anyway?”  He talked about how policy makers view science.  (Obviously, many are perplexed.)  He forgot that the universe and Mother Nature are vastly mysterious things, which are often more complicated than human understanding, but sensitive to human actions at the same time.  Yes, science is perplexing.

Mr. Isenberg talked about “independent science” and “combat science,” as though they were two different things.  To borrow a legal term, science is not self-executing.  Then he asked: “How do we know when we are using the best-available science”?  His answer: “When it is good enough to avoid doing something stupid.”  Clearly, we have yet to reach that point.  The problem has been in choosing to do the best thing, not that good choices or unknown or not “available.”  He then quoted Churchill:  “America will always do the right thing after trying everything else first”At least we have gotten past the point where we thought the world is flat.  It is all very perplexing.

Mr. Isenberg concluded by suggesting: “It’s the notion that scientists live looking farther out than the rest of us do with the gift of foresight that if properly utilized, can inform, educate, and ultimately motivate policy makers.”   He forgets that ultimately policy makers must trust scientists to get the job done.  Example: the Trinity Project and the atomic bomb in the 1940’s.  As long as water managers and policy makers lead the science, the Delta’s problems will not be solved.

The Delta Science Program

Clifford Dahm, former lead scientist for the Delta Stewardship Council, spoke on his Delta Science Program, which was forced upon us in the 2009 Delta Reform Act to ensure water and environmental policy are guided by the “highest caliber” science.  He spoke on the program’s Independent Science Board, outsiders who meet once a year to review “our science”.  He spoke on their Adaptive Management Program, which ensures that we evaluate everything and learn nothing.  He spoke on the program’s efforts to coordinate science and inform decision makers, and to develop and implement the Delta Science Plan and promote the Science Action Agenda.  He talked about their modeling efforts: “There’s just a lot of ways that modeling could be moved forward, and I hope that in the next two years, we can actually come back to you and say that some of our modeling efforts have shown greater fruition as time goes on.  We were talking about the idea of potentially a modeling center or a co-laboratory to get modelers together.”  Those would be the two years after which we will have new water quality standards, new biological opinions, and new tunnel-boring machines in the Delta, as well as several newly extinct native fish species.  They would also be the two years after 20 years of effort starting with the CalFed Bay-Delta Program.

A Great Question

U.C. Davis fisheries biologist Peter Moyle then addressed the question:  “How has your research program and the data it has produced over the last 35 years been used to develop solutions for conserving aquatic resources in Delta?”  He quoted the 1998 Strategic Plan:

This strategic plan, if followed, should lead to an orderly and successful program of adaptive ecosystem restoration….  The Strategic Plan Core Team has high expectations for the Ecosystem Restoration Program.  There is no turning back and the team anticipates that in 20-30 years many habitats will be restored, endangered species will become abundant enough to be delisted, and conflicts will be lessened , even in the face of population growth and increasing demands on resources.

In addressing the posed question, he then remarked:

In retrospect, now that almost 20 years has past since that was written, the statement almost seems tongue in cheek because clearly that has not happened.  I continue to help write reports that recommend how to improve the Delta ecosystem and frankly I don’t see much progress being made, as the delta smelt trends so eloquently attests…  the reality is that the Delta has continued to deteriorate as a habitat for native fishes, despite my research and despite many proposals for solutions.

His experience, like that of so many other long-time Delta scientists, is that few if any of the specific recommendations in the Strategic Plan have been implemented or completed.  Science has done its job, and scientists have long awaited action.  Policy makers and managers have failed us, not the science.

The use of science in complex public policy decision making

Chair of the State Water Board Felicia Marcus spoke on the use of science in decision making.  She suggested to scientists:  “Dare to recommend, but don’t decree …  Retain your scientific integrity but dare to make recommendations.  At the same time, own your power and be responsible with it and have empathy for the decision makers who have to balance, even as you would have them respect you.”  This is a very tough sell for scientists who have not been listened to for decades.  What will she and her Board do with two more rounds of recommendations on the Delta tunnels and the Bay-Delta Plan?  Will her Board be as transparent and methodical in their balancing as the scientists are in making their recommendations?

Chair Marcus further stated:

We’re entering the era of adaptive management that requires all of the above as well as integrating social sciences into our work … To make adaptive management work, we all have to learn how to be better ‘egosystem’ managers in order to be better ecosystem managers in the real world over time, versus lurching from sound bite to sound bite or wringing our hands that other players just don’t get it.

Sorry, but that’s not the problem.  It gives the policy makers and the managers too much credit and scientists too little.  Very few scientists think that managerial ignorance or lack of cognition is the biggest problem.  Rather, it’s that scientists have endured decades of adaptive management in which their lessons and caveats have on the whole been subsumed to the social sciences of politics and economics.  There are plenty of scientists throughout the resource agencies and non-profit groups who are extremely articulate and who have great senses of humor and social skills.   That hasn’t changed the outcomes: fish and other parts of the Bay-Delta aquatic ecosystem are in crisis, and the agricultural economy and other values against which the ecosystem is “balanced” are thriving..  And that balance sheet is really nothing to smile about.

Fundamental Needs of Central Valley Fishes – Part 1c: Spring River Flows

In the coming months and years, regulatory processes involving water rights, water quality, and endangered species will determine the future of Central Valley fishes.

To protect and enhance these fish populations, these processes will need to address four fundamental needs:

  1. River Flows
  2. River Water Temperatures
  3. Delta Outflow, Salinity, and Water Temperature
  4. Valley Flood Bypasses

In this post, I summarize a portion of the issues relating to River Flows:  spring flows.  Previous posts covered fall and winter flows.

River Flows – Spring

River flows in spring drive many natural ecological processes in the Central Valley related to Sierra snowmelt.  Winter-run and spring-run salmon, steelhead, Pacific lamprey, and white and green sturgeon ascend the rivers from the ocean during the spring snowmelt season.  Spring-run salmon arre able to migrate upstream in the high water to hold until late summer spawning.  Winter-run salmon and sturgeon spawn in the Sacramento River below Shasta that same spring.  Pacific lamprey spawn in streams throughout the Valley in spring.  Juveniles, and remnant yearlings of all these species spawned in the previous year, head to the ocean in the high flows.  In the Valley, the spring snowmelt and rains swell the rivers for the annual runs of Delta smelt, splittail, American shad, Sacramento suckers, and striped bass.   In the Bay-Delta, spring flows spur annual productivity that sustains juvenile longfin smelt, Delta smelt, fall-run salmon, green and white sturgeon, striped bass, American shad, and splittail, as well as many resident and estuarine fishes and their food supply.

Much of the Valley’s snowmelt is captured in mountain and Valley rim reservoirs, breaking the link between the ocean and mountains.  In the lower Sacramento River below Shasta Reservoir, spring snowmelt flows are markedly reduced by retention of snowmelt in the reservoir (Figure 1).  The Feather River, the main Sacramento River tributary, are similarly affected (Figure 2).  In the San Joaquin River watershed, absence of flows sourced in spring snowmelt is also severe (Figure 3).  The capture of snowmelt not only reduces flow in Valley rivers and the Bay-Delta, but also reduces sediment load, river scour, water depths and velocities.  It raises water temperatures and limits the extent of natural floodplain inundation.  All of these are important ecological processes on which native fishes depend.

Figure 1. Pre-and post-Shasta flows in the lower Sacramento River near Red Bluff (Bend Bridge gage). Note that nearly all the peak spring snowmelt flows have been removed below Shasta in all year types. (USGS gage data)

Figure 1. Pre-and post-Shasta flows in the lower Sacramento River near Red Bluff (Bend Bridge gage). Note that nearly all the peak spring snowmelt flows have been removed below Shasta in all year types. (USGS gage data)

Figure 2. Pre- and post-Oroville Reservoir flows in the lower Feather River. (CDWR data)

Figure 2. Pre- and post-Oroville Reservoir flows in the lower Feather River. (CDWR data)

Figure 3. Spring snowmelt (natural flow – blue line) is retained in New Melones Reservoir except for prescribed irrigation releases and salmon migration flows (orange line – reservoir releases to lower Stanislaus River). (CDEC data)

Figure 3. Spring snowmelt (natural flow – blue line) is retained in New Melones Reservoir except for prescribed irrigation releases and salmon migration flows (orange line – reservoir releases to lower Stanislaus River). (CDEC data)

Under current operations, spring snowmelt into the Valley reservoirs is generally held in storage except for minimum downstream flow requirements, agricultural demands, Delta inflow and outflow to meet water quality standards, and minimum flow specifications for endangered fish in biological opinions.  Flow releases for agriculture and fish are generally re-diverted soon after release, thus resulting in further reduction of downstream flows (this is the case for  the lower Sacramento River in Figure 1, the lower Feather River in Figure 2, and lower Stanislaus River in Figure 3).  Critical conditions often appear below these diversions in the lower Sacramento River (Figure 4), in the lower San Joaquin River, and in outflow from the Delta to the Bay.

What is needed are spring releases (spills) from the major Valley reservoirs to the major rivers below dams that carry at least in part to the Bay, to stimulate and sustain migrations of the adult and juvenile anadromous fish throughout the Valley.  Water releases timed to the natural flow pulses would stimulate migration, providing even more flow and stimulus for young anadromous fish from all the Valley rivers to pass successfully through the Delta and Bay to the ocean.

Figure 4. River flow (cfs) in lower Sacramento River below major irrigation diversions in four recent years representing four water-year types. Green line represents minimum flow needed to maintain a semblance of essential ecological processes in the lower river. Red line represents preferred minimum level protecting ecological processes. May-June flow is generally depressed except in wet years.

Figure 4. River flow (cfs) in lower Sacramento River below major irrigation diversions in four recent years representing four water-year types. Green line represents minimum flow needed to maintain a semblance of essential ecological processes in the lower river. Red line represents preferred minimum level protecting ecological processes. May-June flow is generally depressed except in wet years.

Winter-Run Chinook Salmon Status – End of 2016

The prognosis for winter-run Chinook salmon is not good following very poor survival of the 2014 and 2015 spawns in the Sacramento River below Shasta Dam.   The run had been recovering after the 2007-2009 drought (Figure 1).  However, year class production suffered in the 2012-2015 drought, culminating with the year class (spawn) failures in 2014 and 2015 (Figure 2) caused by egg stranding and high water temperatures.  Run size and juvenile production/survival estimates for 2016 are as yet incomplete, but production of juveniles as estimated from Red Bluff rotary screw trap data indicates some improvement over 2014-2015.1 The somewhat higher number of recruits produced in 2013 likely boosted the spawning run in 2016.

With water year 2017 starting out as a wet year with considerable flooding, conditions for the emigration of the 2016 year class should be optimal.  If wet conditions persist, spawning and rearing this spring and summer for the 2017 year class should also be optimal.  Planned release of 600,000 winter-run hatchery smolts in the coming weeks coincident to high Sacramento River flows also bodes well for the 2016 spawn and the future 2019 run.  However, the prognosis for the 2017 and 2018 runs remains in doubt because of the above-mentioned 2014 and 2015 year class failures.

Additional insight into the future is possible by taking a closer look at the population’s spawner-recruit relationship that I prepared for the past four decades (Figure 3).  Recruitment appears to be a function of both the number of spawners three years prior to any given year and environmental conditions between spawning and emigration in a given year.  (Other factors such as ocean conditions may also add to variability in the data.)  The recruits-per-spawner ratio is higher three years after wet years than three years after dry years.  The runs in 2017 and 2018 are likely to be severely depressed because of extremely poor 2014 and 2015 recruitment, and may possibly be as low as those produced after the 1987-91 drought (only 100-200 wild spawners).

For further reading on winter-run status see:

  1. http://deltacouncil.ca.gov/sites/default/files/2015/11/Vogel%20White%20Paper-%20Potential%20effects%20of%20CVP %20Ops%20on%20winter%20run%20Chinook%20egg%20incubation%202015.pdf
  2. http://www.westcoast.fisheries.noaa.gov/stories/2015/23_12232015_winter_chinook_math.html
  3. http://www.nmfs.noaa.gov/stories/2015/09/spotlight_chinook_salmon.html
  4. http://mavensnotebook.com/2015/12/15/conserving-chinook-salmon-at-the-southern-end-of-their-range-challenges-and-opportunities/
Figure 1. Winter-run Chinook salmon escapement (run size) into upper Sacramento River near Redding, CA from 1974-2015. (Data Source: http://www.dfg.ca.gov/fish/Resources/Chinook/CValleyAssessment.asp)

Figure 1. Winter-run Chinook salmon escapement (run size) into upper Sacramento River near Redding, CA from 1974-2015. (Data Source: http://www.dfg.ca.gov/fish/Resources/Chinook/CValleyAssessment.asp)

Figure 2. Survival of winter-run year classes below Shasta Dam from 1996-2015. The water temperature standard for the Sacramento River near Red Bluff was weakened during 2012-2015 drought. The severely weakened water quality standard in 2014 and 2015 led to poor survival and virtual loss of two year classes. (Source: http://www.waterboards.ca.gov/waterrights/water_issues/programs/drought/sacramento_river/docs/nmfs_yip_03182016_ppt.pdf)

Figure 2. Survival of winter-run year classes below Shasta Dam from 1996-2015. The water temperature standard for the Sacramento River near Red Bluff was weakened during 2012-2015 drought. The severely weakened water quality standard in 2014 and 2015 led to poor survival and virtual loss of two year classes. (Source: http://www.waterboards.ca.gov/waterrights/water_issues/programs/drought/sacramento_river/docs/nmfs_yip_03182016_ppt.pdf)

Figure 3. Winter-run Chinook spawners versus number of spawners three years later (recruits) for years 1974 through 2012. Selected wet year spawn dates shown in blue. Selected dry year spawn dates shown in red. (Data source: http://www.dfg.ca.gov/fish/Resources/Chinook/CValleyAssessment.asp)

Figure 3. Winter-run Chinook spawners versus number of spawners three years later (recruits) for years 1974 through 2012. Selected wet year spawn dates shown in blue. Selected dry year spawn dates shown in red.
(Data source: http://www.dfg.ca.gov/fish/Resources/Chinook/CValleyAssessment.asp)

Splittail Status – End of 2016

The prognosis for splittail was not good in 20151 after four years of drought and little recruitment since 2011. The below-normal water year in 2016, with its limited winter flooding, brought no apparent recovery in the Fall Midwater Trawl Index (Figure 1). Summer salvage (Figure 2) indicated that there was some production in 2016, although salvage was two orders of magnitude lower than the previous normal water year 2010 (Figure 3) and three orders of magnitude less than the previous wet water year 2011 (Figure 4).

If water year 2017 were to continue on its current trajectory and become a wet year with widespread flooding, conditions for splittail spawning and rearing this winter and spring would be optimal. A positive response in salvage, Fall Midwater Trawl Survey, and FWS Seine Survey would indicate some form of recovery in the population. However, a lack of response on the order of that which occurred in 2011 would be a signal that the population is in dire straits and at risk of recruitment failure and eventual extinction. In the absence of a 2011-magnitude response in the next wet year, the fisheries agencies should conduct a comprehensive review to evaluate whether to re-list2 splittail under the federal and state endangered species acts.

Figure 1.  Splittail Fall Midwater Trawl Survey Index 1967-2016.  (Data Source)

Figure 1. Splittail Fall Midwater Trawl Survey Index 1967-2016. (Data Source3)

Figure 2.  Splittail salvage in 2016.  Export rate for federal and state pumping plants.  (Source )

Figure 2. Splittail salvage in 2016. Export rate for federal and state pumping plants. (Source4)

Figure 3.  Splittail salvage in 2010.  Export rate for federal and state pumping plants.  (Source )

Figure 3. Splittail salvage in 2010. Export rate for federal and state pumping plants. (Source5)

Figure 4.  Splittail salvage in 2011.  Export rate for federal and state pumping plants.  (Source )

Figure 4. Splittail salvage in 2011. Export rate for federal and state pumping plants. (Source6)

  1. http://calsport.org/fisheriesblog/?p=1126
  2. Splittail were de-listed in 2003. On October 7, 2010, the USFWS found that re-listing of splittail was not warranted (75 FR 62070). The splittail is designated as a species of special concern by the California Department of Fish and Wildlife.
  3. https://www.wildlife.ca.gov/Conservation/Delta/Fall-Midwater-Trawl
  4. https://www.wildlife.ca.gov/Conservation/Delta/Salvage-Monitoring
  5. https://www.wildlife.ca.gov/Conservation/Delta/Salvage-Monitoring
  6. https://www.wildlife.ca.gov/Conservation/Delta/Salvage-Monitoring

Striped Bass Status – End of 2016

The prognosis for stripers was not good in 20151 after four years of drought. The normal water year in 2016 brought only minor improvement in recruitment of juveniles into the population, but recruitment remains near record lows (Figures 1-3). The wetter 2016 started with higher juvenile production, but that stalled by late spring. Striped bass salvage at south Delta export facilities showed typical patterns, with about 10% of the numbers salvaged in year 2000 and two primary peaks in salvage – late spring/early summer and late fall (Figure 4).

The Fall Recruitment Index of juveniles into the population as derived from the Fall Midwater Trawl Survey (Figure 2) compared with the prior Summer Townet Survey (Figure 1) indicates a strong positive relationship (Figure 5). The year class strength is very much dependent on the number of young starting the summer, which in turn is likely related to the number of eggs laid in spring and subsequent survival of larvae hatched to the early summer juvenile stage as measured in the Summer Townet Survey. Subsequent survival to the fall appears related to summer habitat conditions, for which a good indicator is Delta outflow. High relative survival to fall in 1998 and 2006 (labeled blue in Figure 5) is likely due to these summers’ higher Delta outflow (Figure 6) and related Delta conditions including export levels (Figure 4). The 2010 and 2016 fall indices were likely suppressed by low outflow, high exports, and resulting poor in-Delta survival, indicated by high salvage numbers. Likewise summer and fall indices in drought years 2007, 2014, and 2015 were likely depressed (Figure 5) by these same factors.

The above patterns and observations are very important because the striped bass remain an important indicator of Bay-Delta Estuary ecological health.

Figure 1.  Striped bass Summer Townet Survey Index 1959-2016.  (Data Source )

Figure 1. Striped bass Summer Townet Survey Index 1959-2016. (Data Source2)

Figure 2.  Striped bass Fall Midwater Trawl Survey Index 1967-2016.  (Data Source )

Figure 2. Striped bass Fall Midwater Trawl Survey Index 1967-2016. (Data Source3)

Figure 3.  Striped bass Fall Midwater Trawl Survey Index 2000-2016. (Same source as Figure 2)

Figure 3. Striped bass Fall Midwater Trawl Survey Index 2000-2016. (Same source as Figure 2)

Figure 4.  Striped bass salvage at south Delta fish facilities in 2016.  Export rate is shown as acre-feet (~2 times rate in cfs).  (Data Source )

Figure 4. Striped bass salvage at south Delta fish facilities in 2016. Export rate is shown as acre-feet (~2 times rate in cfs). (Data Source4)

Figure 5. Striped bass Fall Midwater Trawl Survey Index (log10[index+1]) versus prior Summer Townet Index (log10).  Select years labeled, with color of number showing year type: blue=wet, green=normal, and red=critically dry.

Figure 5. Striped bass Fall Midwater Trawl Survey Index (log10[index+1]) versus prior Summer Townet Index (log10). Select years labeled, with color of number showing year type: blue=wet, green=normal, and red=critically dry.

Figure 6.  June through August Delta outflow in 1998, 2006, and 2010.

Figure 6. June through August Delta outflow in 1998, 2006, and 2010.

Delta Smelt at Risk – 1/5/17

The conflict continues between the Smelt Working Group (SWG) and the designated protector of the Delta smelt, the US Fish and Wildlife Service (FWS), over the amount of Delta exports allowed under existing Delta conditions.  The SWG recommends exports of no more than 2000 cfs, while the FWS continues to allow exports of 5000-6000 cfs (about half capacity), contrary to  the rules for Delta exports in its own smelt biological opinion.  The SWG notes that adult smelt continue to be captured in trawls in the central Delta (in surprising numbers), where smelt are at high risk of being drawn to the south Delta pumping plants or of eventually spawning in the central Delta where their offspring will be vulnerable to the export pumps.  The FWS is committed to allowing moderate exports as long as no adults are captured at the pumping plants’ fish salvage facilities (which would indicate it is too late to do anything other than to shut down the pumps). The National Marine Fisheries Service limits exports to the present 5000-6000 cfs level as of January 1, consistent with rules in its own biological opinion to protect juvenile salmon migrating down the Sacramento River.

Despite high Sacramento River inflows into the Delta of 30,000 to 50,000 cfs in the past two weeks, the smelt move from the Bay into the Delta by surfing the tides – that is, by moving upstream on incoming tides.  Flood tide velocities shown in Figure 1 indicate the adult smelt can readily “surf” into the Delta until they come up against the strong flows of the Sacramento River and its inflow channels that overwhelm the tidal flows.  In the south Delta, where limited flow has been coming down the San Joaquin River, export pumping plants accentuate the negative flood tide velocities and reduce ebb tide velocities.  This further increases the risk that adult smelt will be drawn to the south Delta.  Only time will tell if this risky FWS strategy protects the endangered Delta smelt during this potential comeback year.

Figure 1. Flood tide channel current velocities in feet/second in early January 2017. Arrows depict current direction on flood tides. Sacramento River net downstream flow was 30,000-50,000 cfs, which overwhelmed the flood tide. Light blue dots are flow gaging stations. Basemap source with gaging stations is DWR/CDEC.

Figure 1. Flood tide channel current velocities in feet/second in early January 2017. Arrows depict current direction on flood tides. Sacramento River net downstream flow was 30,000-50,000 cfs, which overwhelmed the flood tide. Light blue dots are flow gaging stations. Basemap source with gaging stations is DWR/CDEC.

Longfin Smelt Status – End of 2016

The longfin smelt population in the Bay-Delta reached a near record low index in 2016 (Figures 1 and 2).  The index was 7, slightly higher than the record low index of 4 in fall 2015.  There is a strong positive spawner (fall index two years prior) to recruitment (fall index) relationship (Figure 3).  Recruitment is strongly related to the number of spawners (likely the number of eggs spawned).  Recruits-per-spawner is also strongly influenced by wet or dry year conditions; in other words, first-year survival is higher in wetter years.  The poor fall 2015 and 2016 indices indicate that recruitment in 2017 and 2018 is likely to continue at record low levels.  Adult longfin (presumably some two-year-old spawners) were collected in the Bay trawl survey in December 2016.  Mid-January 2017 larval smelt surveys will be the first indication of recruitment into the population in 2017.  Water year 2017 has been a wet year to date, so some positive response in recruitment could potentially occur.

We will be keeping a close look at longfin recruitment in 2017, especially with new less stringent export restrictions mandated in recent legislation for the implementation of the two federal biological opinions that apply to Delta water project operations.  So far, no adult longfin have been collected in salvage at the south Delta export facilities.

sSouth Delta xEexport fish salvage facilities. Figure 1. Longfin smelt Fall Midwater Trawl indices 1967-2016. Source: CDFW.

Figure 1. Longfin smelt Fall Midwater Trawl indices 1967-2016. Source: CDFW.

Figure 2. Longfin smelt Fall Midwater Trawl indices 2000-2016. (Note: 2007=13; 2015=4; 2016=7) Source: CDFW.

Figure 2. Longfin smelt Fall Midwater Trawl indices 2000-2016. (Note: 2007=13; 2015=4; 2016=7) Source: CDFW.

Figure 3. Longfin smelt Fall Midwater Trawl Index (Recruits) vs two-year-prior index (Spawners), log10 scales. Wet years are blue labelled; dry years are red labelled.

Figure 3. Longfin smelt Fall Midwater Trawl Index (Recruits) vs two-year-prior index (Spawners), log10 scales. Wet years are blue labelled; dry years are red labelled.