Scott River Coho Salmon Run – Status Fall 2019

The Scott River Coho salmon population is one of the last remaining self-sustaining wild Coho salmon runs in California and in the Southern Oregon Northern California Coho (SONCC) Evolutionarily Significant Unit (ESU).  The SONCC ESU is listed as “threatened” under the federal and California endangered species acts.  The ESU includes the Rogue River in Oregon and the Klamath River in California.

The Scott Coho run is the major wild Coho population in the Klamath River system.  Scott Coho spawn and rear in Scott Valley, once called “Beaver Valley,” located near Fort Jones.  The run has numbered over 1,000 adult Coho spawners as recently as 2013, but numbered less than 100 as recently as the 2008-09 drought years (Figure 1).

Scott Coho include three distinct sub-populations that have developed because the vast majority of spawners are three years old.  One subgroup, the 2007-2010-2013 sub-group, dominated the population in the recent past, but declined sharply in 2016.  The other two sub-groups have increased slightly since 2008 and 2009 lows.

The spawner-recruit relationship (Figure 2) shows a generally positive relationship between the number of spawners and recruits three years later for each sub-group and the overall population with one distinct outlier (the sharply lower 2016 run).  So why was the 2013 run so high and the brood-year 2013 run in 2016 so poor?

1.      2013’s Good Run

The 2013 run (brood year 2010) got off to a great start in wet water year 2011.  Flows for the fall 2010 spawning run were good from November through January [Figure 3), which ensured spawner access and good spawning conditions throughout Scott Valley.  Flows were also good through the spring and fall of 2011 (Figure 4), ensuring good smolt production and a subsequent strong run in 2013.

2.      2016’s Poor Run

The strong run in 2013 spawned in brood year 2013, which got off to a rocky start in dry water year 2013-14.  Flows in fall-winter 2013-14 encountered by the strong 2013 run were very low through the early winter spawning season (Figure 5), leading to an unusually protracted run of adult spawners (Figure 6) and poor accessibility to good spawning areas.  Spawning habitat quality and quantity likely also suffered from low flows.  Flows were then very low from spring through fall of 2014 (Figure 7), likely resulting in poor over-summer survival and low smolt production for brood year 2013.

In conclusion, the Scott Coho salmon population continues to suffer from low seasonal streamflow, especially in drought years like water year 2013-14.  The population would benefit from improved summer-through-fall streamflows.  It will also benefit from the watershed habitat restoration actions being implemented by landowners, CalTrout,  the Scott River Watershed Council, Siskiyou RCD, Scott River Water Trust, California Department of Fish and Wildlife, Quartz Valley Indian Reservation, and other stakeholders.

Figure 1. Escapement of adult Coho salmon to the Scott River from 2007 to 2019. Data source: CDFW, Yreka, CA.

Figure 1. Escapement of adult Coho salmon to the Scott River from 2007 to 2019. Data source: CDFW, Yreka, CA.

Figure 2. Spawner-recruit relationship for Scott River Coho salmon. The number represents recruits (spawner counts) for that year versus spawners counts from three years earlier. For example: “13” represents spawner counts (recruits) in fall 2013 versus spawner numbers three years earlier in 2010. Number color represents different spawner subgroups (blue=subgroup 10-13-16-19). The Red circle highlights significant outlier in 2016. The Yellow line is trend-line for years other than 2016.

Figure 3. USGS gaged daily average flow (log scale) in lower Scott River, Klamath River tributary, 9/1/2010-2/1/2011, with 78 year average daily median flow for that date.

Figure 4. USGS gaged daily average flow (log scale) in lower Scott River, Klamath River tributary, 4/1/2011-11/1/2011, with 78 year average daily median flow for that date.

Figure 5. USGS gaged daily average flow (log scale) in lower Scott River, Klamath River tributary, 9/1/2013-2/1/2014, with 78 year average daily median flow for that date.

Figure 5. USGS gaged daily average flow (log scale) in lower Scott River, Klamath River tributary, 9/1/2013-2/1/2014, with 78 year average daily median flow for that date.

Figure 6. Scott River adult salmon collection weir counts of Coho salmon for fall-winter 2013-14. Data source: CDFW Yreka, CA.

Figure 7. USGS gaged daily average flow (log scale) in lower Scott River, Klamath River tributary, 4/1/2014-10/31/2014, with 78 year average daily median flow for that date.

 

 

Essential Needs for the Recovery of Endangered Winter-Run Salmon

Summer spawning and egg incubation water temperatures in the upper Sacramento River below Shasta Dam is a well-known and documented key to the recovery of winter-run salmon Chinook salmon. In a December 2018 post, I noted the importance of early-fall flows to support the emigration of juvenile winter-run salmon from spawning and early rearing areas of the upper Sacramento River near Redding. In this post, I add another measure to the list of essential needs.

  • Late-fall flows – Flows to move winter-run juveniles from the upper and lower river into and through the Delta in the late fall.

What kind of late-fall flows are specifically needed? The type that occurred in December 2019 from a spate of storms (Figure 1). The 10,000+ cfs flow in the lower Sacramento River got wild winter-run salmon smolts through the lower Sacramento River, as seen from the Knights Landing screw-trap catches. The 20,000+ cfs early-December pulse of Delta outflow got wild winter-run salmon smolts moving through the Bay toward the ocean, as seen in the Chipps Island Suisun Bay trawl catches.

I have previously recommended extending Fall X2 Delta outflow protections1 and reducing Delta exports2 to help the winter-run smolts during their emigration to the ocean. As it was, 10,000+ cfs exports in the latter half of December 2019 took over half of the potential Delta outflow. Figure 1 clearly shows the importance of the late-fall flows to the emigration of winter-run.

Observed patterns of winter run emigration provide further evidence of the need for flows in the late fall. Figure 2 shows late fall 2017 conditions when there was no late fall flow pulse. The movement of winter-run smolts through the Bay was delayed, occurring in small spurts from late January through March. There is no doubt that one-to-three-month delays in smolt migrations from the river and Delta to the ocean are detrimental to the population and to recovery.

Figure 3 shows the latefall flow pattern over the past decade. Recovery of winter-run salmon depends on protecting the flow pulses. The tendency is to export as much of the first flows of the water supply season as possible and get it stored in south-of-Delta reservoirs. Most of the late-fall rainfall was already captured in upstream reservoirs, so these flow pulses are just a fraction of Central Valley’s natural flows.

A close look at Figure 3 shows minimal Delta outflow in the late fall of 2011 and 2017. Both years were just coming off wet water years. Shasta Reservoir had above-average storage for December in both years (>3 MAF, two-thirds full). Modest commitments of reservoir water could have greatly benefitted winter-run emigration. Inflows to Shasta reservoir in December of both of those two years were over 200 TAF. An added release of less than half that inflow (100 TAF) could have provided five days of 10,000 cfs pulse flow to the December release pattern in both years. Such a pulse flow, in combination with reduced Delta exports (Figure 4), would have provided five days of 20,000+ cfs Delta outflows in December 2011 and 2017 to support wild winter-run smolt emigration and winter-run recovery.

Figure 1. Catch patterns of juvenile wild winter-run salmon in the upper Sacramento River at Red Bluff, the lower Sacramento River at Knights Landing, and at Chipps Island in the upper Bay in fall 2019. Red circles denote catch peaks associated with fall pulsed flows.

Figure 2. Catch patterns of juvenile wild winter-run salmon in the upper Sacramento River at Red Bluff, the lower Sacramento River at Knights Landing, and at Chipps Island in the upper Bay in fall-winter 2017-18. Red circles show dispersed timing of emigration and lack of large catch peaks in the absence of fall pulsed flows.

Figure 3. Delta outflow in late fall 2010-2019. Note lowest flows were in 2011, 2013, 2015, and 2017.

Figure 4. December 2011, 2017, and 2019 south Delta exports at the state Banks (HRO) and federal Tracy (TRP) pumping plants. Capacities are 7500 and 4400 cfs, respectively. Note the extremely high and unusual December 2019 exports.

Downward Trend in San Francisco Bay Longfin Smelt

In my last posts on longfin smelt, I expressed some optimism about their recovery from the 2013-2015 drought based on 2017 and 2018 population data (Figure 1).1 I have changed my mind. In this wet water year 2019, the longfin have again crashed.

The long-term trend over four wet-year November adult trawl surveys, including this year (2019), continues downward (Figures 2-5). The trend portrays the underlying strong spawner-recruit relationship: the number of spawners (eggs) is the key factor that determines recruits. On top of that, poor recruitment in drier years (Figure 6) is driving recruitment-per-spawner down. There is 10-100 times higher recruitment from wetter years.

What is it about both dry years and wetter years like 2019 that is so bad? It is low Delta outflow and high exports in the November-December period.

Longfin smelt spawn in November-December in fresh water.2 When their freshwater habitat is in the San Joaquin channel in the central Delta upstream of Jersey Point (See location in Figure 2, Figures 7 and 8), the newly hatched larvae are highly susceptible to unlimited November and December exports. Although 2019 was a wet year, these conditions were present in November and December (Figures 9 and 10).

The prognosis for longfin smelt under current and planned water operations in the Delta is grim. The state and federal water projects need to increase Delta outflow and reduce exports in November and December to reduce spawning of longfin smelt in the central and south Delta.

Figure 1. Fall Midwater Trawl Index for longfin smelt, 1967-2018. Source: http://www.dfg.ca.gov/delta/data/fmwt/indices.asp

Figure 2. Catch distribution of longfin smelt adults in the November 1998 fall midwater trawl survey.

Figure 3. Catch distribution of longfin smelt adults in the November 2011 fall midwater trawl survey.

Figure 4. Catch distribution of longfin smelt adults in the November 2017 fall midwater trawl survey.

Figure 5. Catch distribution of longfin smelt adults in the November 2019 fall midwater trawl survey.

Figure 6. Longfin Recruits (Fall Midwater Trawl Index) vs Spawners (Index from two years prior) in Log10 scale. The relationship is very strong and highly statistically significant. Adding Delta outflow in winter-spring as a factor makes the relationship even stronger. Recruits per spawner are dramatically lower in drier, lower-outflow years (red years). Spawners in 2017 and 2018 were at record low levels. Recruits in 2011 and 2017 were relatively high because the Fall X2 provision in the 2008 Biological Opinion was implemented. Source: http://calsport.org/fisheriesblog/?p=2513.

Figure 7. Salinity (EC) in November and December 2017 at Jersey Point in the lower San Joaquin River channel of the west Delta. Spawning would occur in fresh water (below 500 EC).

Figure 8. Salinity (EC) in November and December 2018 at Jersey Point in the lower San Joaquin River channel of the west Delta. Spawning would occur in freshwater (below 500 EC), which occurred upstream of Jersey Point.

Figure 9. Salinity (EC) in November and December 2019 at Jersey Point in the lower San Joaquin River channel of the west Delta. Spawning would occur in freshwater (below 500 EC), which occurred upstream of Jersey Point.

Figure 10. Tidally filtered flow in two channels in the lower San Joaquin River upstream of Jersey Point, portraying net flows toward to the south Delta export pumps.

 

The Final Straw for Delta Smelt; Another Dagger for Longfin

Delta smelt and longfin smelt were not protected in the Delta in November-December 2019. High south Delta exports (Figure 1) and associated highly negative Old and Middle River (OMR) flows (Figure 2) pulled the spawning adult smelt toward the export pumps, likely significantly compromising what is left of the two populations. High exports and negative flows also pulled saltwater from the west Delta into the central Delta (Figures 3 and 4). This forced smelt to spawn further upstream in the fresher water of the central, east, and south Delta, sealing the fate of the numerous larval longfin smelt spawned there to the export pumps this winter. Young Chinook salmon, especially listed winter-run and spring-run entering the Delta in December, were also jeopardized.1

These circumstances were not allowed under the federal 2008 Delta smelt biological opinion (Figure 5) or the state’s longfin smelt incidental take permit (Figure 6). The new October 2019 Biological Opinion (BO) for the operation of the Central Valley Project (issued under the federal Endangered Species Act) does not preclude high exports or highly negative OMR flows. The pending new state Incidental Take Permit (ITP) for the operation of the State Water Project (to be issued under the California Endangered Species Act) follows the requirements of the federal BO for Delta smelt.

Given the December distribution of adult longfin smelt (Figure 7) and the likely distribution of the few remaining adult Delta smelt based on prior year surveys (Figure 8), the Smelt Working Group (SWG), Water Operations Management Team (WOMT), and the Director of the California Department of Fish and Wildlife (CDFW) should have limited south Delta exports in December. They did not.

The Trump administration’s new biological opinions simply do not protect these fish. The pending new state ITP for protection of these fish gives the Director of the California Department of Fish and Wildlife the last word in ordering changes to OMR flows. The CDFW Director’s non-decision in 2019 is a good indication of the level of protection that is likely under the new state ITP.

Figure 1. December 2019 state (HRO) and federal (TRP) south Delta exports. Note the maximum total rate of approximately 11,400 cfs was reached in the latter half of December.

Figure 2. December 2019 Old and Middle River (OMR) net daily flows.

Figure 3. Salinity (EC) in central Delta in December 2019.

Figure 4. Salinity (EC) in Old River in the south Delta in December 2019.

Figure 5. Page 281 of 2008 federal biological opinion for Delta smelt.

Figure 6. Page 10 of 2009 state Incidental Take Permit for longfin smelt.

Figure 7. Distribution of longfin smelt in December 2019 midwater trawl survey. These numbers are very low and show the present depressed level of the population.

Figure 8. Distribution of Delta smelt in December 2011 midwater trawl survey
showing likely distribution of remaining Delta smelt in 2019 (midwater trawl
survey found no Delta smelt in December 2019).

 

San Joaquin Fall-Run Salmon – Status Fall 2019

In previous updates in 2016 and 2017, I remarked on progress toward increasing San Joaquin watershed salmon runs during the recent 2013-2015 drought period.  I attributed the improvements to several positive factors:

  1. Increased production from Mokelumne and Merced state hatcheries. Both the Stanislaus and Tuolumne runs benefitted from strays from the two hatcheries, as well as from strays from the three Sacramento River hatcheries (Battle Creek, Feather, and American).
  2. River and Delta flow improvements in spring and fall mandated by federal biological opinions.
  3. Stronger runs in the Stanislaus River from improved flow and water temperature regimes in the Stanislaus and in the San Joaquin below the mouth of the Stanislaus. Fall temperatures below 60oF in the Stanislaus and below 65oF in the San Joaquin proved beneficial to the Stanislaus run, likely by attracting hatchery salmon as well as wild strays from the Merced and Tuolumne rivers.

I also attributed past very poor runs to drought conditions during rearing and during adult spawning runs, exactly the conditions of the 2015 run.  However, the 2015 run was much better than expected, likely because of hatchery strays.

In this post, I update the previous assessments with new information on the 2016-2018 runs.  The 2016 and 2017 runs were the product of rearing conditions in the 2014 and 2015 critical drought years, as well as wetter-year fall adult migration conditions.  The 2018 run was a product of normal-water-year rearing (2016) and adult migration (2018) conditions.

The 2016 and 2017 runs were strong in the Stanislaus and Merced rivers (Figure 1), with both rivers benefitting from hatchery production and strays.  One strong component of the strays was the unusually high proportion of strays from the Battle Creek hatchery, whose managers’ strategy during the 2014-2015 drought was to truck smolts to the Bay.

The 2018 San Joaquin run was lower, but still a strong improvement over the drought-influenced runs in 2007-2011 (Figure 1).  Spring rearing conditions in 2016 and fall adult migration conditions in 2018 were generally better than they were during the critical drought years.  Also, most of the Mokelumne and Merced hatchery smolts were released to the Bay and west Delta, respectively, in 2016.  However, adult salmon migrating upstream in the fall of 2018 were subject to stressful conditions in the lower San Joaquin River, where high water temperatures were similar to the high temperatures there in 2015 and 2016 (Figures 2-4).

An updated spawner-recruitment relationship is shown in Figure 5.  Runs from 2016-2018 are shown as red-bordered blue dots labelled from 2014-2016, representing rearing-year conditions for these runs.  The recruitment trend remains strong given the generally dry water conditions during the 2012-2016 drought period.  The recent recruitment per spawner remains up to 10-fold higher than in the prior two droughts, 1987-1992 and 2007-2009.  The best explanations for this improvement remains strong hatchery contributions and better hydrology-related habitat and migration conditions prescribed in the 2008-09 federal biological opinions.

The State Water Resources Control Board is in the process of developing biological goals for fall-run Chinook salmon in the lower San Joaquin River and its three salmon-bearing tributaries.  The Board should include goals for escapement as well as the factors that control escapement.

Figure 1. Chinook salmon runs (escapement) in the San Joaquin River from 1975-2018 is made up of components of escapement/run estimates from its three spawning tributaries. Data source: CDFW.

Figures 2 and 3. Fall water temperatures in the lower San Joaquin River downstream of salmon spawning tributaries in 2015, a critical drought year, and 2016, a normal water year.

Figure 4. Fall water temperatures in the lower San Joaquin River downstream of salmon spawning tributaries in 2018, a normal water year. Compare with temperatures in red circles in Figures 2 and 3.

Figure 5. Recruits-per-spawners relationship ((log10X)-2) for San Joaquin River fall-run Chinook salmon 1976-2018. 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 predominantly 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 a blue circle because fall conditions in wet year 1983 were good).