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.

Essential Needs for the Recovery of Endangered Winter-Run Salmon

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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

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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

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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

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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).

Central Valley Salmon Hatchery Release Strategies 2019 Some Good, Some Bad – Some Lessons Not Learned

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Federal and State hatcheries released 32 million juvenile salmon into the Central Valley, the Bay-Delta, and nearby coastal waters in 2019.1 The hatchery programs included spawning and rearing salmon from all four salmon races: fall-run, late–fall-run, winter-run, and spring-run. The hatchery programs have come a long way through decades of adaptive management, but some lessons were not learned. In this post I summarize and discuss the release strategies in 2019 of the seven hatchery programs. In most cases, release strategies were good for smolt survival. Some releases were made into poor flows and high water temperature conditions that would contribute to poor survival from slowed migration, heat stress, starvation, or high predation rates.

Federal Coleman National Fish Hatchery on Battle Creek (Sacramento River)

The Coleman Hatchery released 11 million salmon to the Sacramento River and its major upper river tributary Battle Creek in 2019 (Figure 1). All but the 176,128 released to the Sacramento River near Redding were released at the hatchery into lower Battle Creek. All the fall-run were from brood year 2018 (spawned in fall 2018). The total late-fall-run release for brood year 2018 was 830,000 including 73,952 released in January 2019, with the remainder released in Nov-Dec 2018.

The Coleman hatchery continues to struggle with problems/conflicts associated with making releases too early or too late in the season.2 Early release of younger smaller pre-smolts has led to poor survival and return rates. Late releases can be a problem because of low flows and high water temperature in the lower Sacramento River (Figure 2). The early 2019 releases could have been made later in April, and the early May release could have been supported by a flow pulse from a near-full Shasta Reservoir in this near-record-high storage year.

Figure 1. Summary of Coleman NFH releases in 2019. Note 755,416 late-fall-run smolts from brood year 2018 were also released into Battle Creek in Nov-Dec 2018.

Figure 2. Spring 2019 river flow and water temperature in the lower Sacramento River at Wilkins Slough near Grimes. Red lines denote upstream releases of Coleman NFH fall-run smolts.

State Oroville Feather River Fish Hatchery

The Feather River Fish Hatchery released 9 million salmon smolts to the Feather River and the Bay in 2019 (Figure 3). All of the nearly 2 million spring-run were released into the lower Feather River in March and April. Six million fall-run smolts were released to the Bay. One million fall-run were released into the lower Feather.

Generally, all the smolts were released under favorable conditions. The release of fall-run into the lower Feather in early May occurred under marginal conditions (Figure 4). This late season fall-run smolt release into the Feather River was subject to potential high predation rates in the river and during their migration through the Delta.

The May releases of Feather River fall-run to east San Pablo Bay and the Napa River estuary (Mare Island) are problematic because that area is a major spawning and rearing area for longfin and Delta smelt during the period of releases, especially in wet years like 2019.3 Yearling or smolt-sized Chinook salmon are known to commonly feed on larval and juveniles fish in estuaries in winter and spring.

Figure 3. Summary of Feather River Hatchery releases in 2019.

Figure 4. Spring 2019 river flow and water temperature in the north Delta in the Sacramento River at Freeport.

State American River Nimbus Hatchery

The Nimbus Hatchery released 3.6 million fall-run salmon smolts to the American River and the Bay in 2019 (Figure 5). Approximately 2.2 million fall-run smolts were released to the Bay. Approximately 1.6 million fall-run were released into the lower American River (at Sunrise Boat Ramp).

Generally, all the smolts were released under favorable conditions. The lower American fall-run release in mid-May occurred under marginal conditions (Figure 4). This late season release into the American River was subject to potential high predation rates in the river and during their migration through the Delta.

The May and June releases to east San Pablo Bay (Conoco) and the Napa River estuary (Mare Island) are problematic because that area is a major spawning and rearing area for longfin and Delta smelt during the period of releases, especially in wet years like 2019.4 Yearling or smolt-sized Chinook salmon are known to commonly feed on larval and juveniles fish in estuaries in winter and spring. The early June releases to the Bay occurred under marginal conditions – high water temperatures stressful to young salmon (Figure 6).

Figure 5. Summary of American River River Hatchery releases in 2019.

Figure 6. Water temperature in spring 2019 at east end of San Pablo Bay near Mare Island release site of Nimbus Hatchery trucked fall run smolts.

State Mokelumne River Hatchery

The Mokelumne Hatchery released 6.6 million fall-run salmon smolts to the Mokelumne River, the west Delta, the Golden Gate, and the coast in 2019 (Figure 7). Approximately 4.5 million fall-run smolts were released to the west Delta near Sherman Island. Approximately 1.7 million smolts were released on the coast and near the Golden Gate5. The remainder (400,000) were released into the lower Mokelumne River.

Generally, most of the smolts were released under favorable conditions. One exception, the lower Mokelumne fall-run releases in mid–May, occurred under marginal conditions (Figure 4). This late-season release into the Mokelumne River was subject to potential high predation rates in the river and during their migration through the Delta. With the Delta Cross Channel closed, these lower river releases were further subject to potentially high risk conditions. In fact, no tagged smolts from the mid-May river releases were detected in south Delta salvage monitoring, an indication of poor survival within the Delta.

Another exception, the late-May releases to the west Delta, are problematic because they occurred under marginal survival conditions – subsequent high water temperatures stressful to young salmon in the west Delta and the Bay (Figures 6 and 8).

Figure 7. Summary of Mokelumne River Hatchery releases in 2019.

Figure 8. Water temperature in spring 2019 in Suisun Bay.

State Merced River Hatchery

The Merced Hatchery released 0.7 million fall-run salmon smolts to the west Delta near Sherman Island (Figure 9). Conditions were marginal in terms of water temperature for the May 1 releases (Figure 10).

Figure 9. Summary of Merced River Hatchery releases in 2019.

Figure 10. Water temperature in spring 2019 in west Delta in San Joaquin channel off Sherman Island at Jersey Point.

State San Joaquin Spring-Run Recovery Hatchery

The Salmon Conservation and Research Facility Hatchery near Fresno released 212,000 spring-run salmon smolts into the San Joaquin River in 2019 (Figure 11). Generally, most of the smolts were released under favorable conditions. The late release on May 30, however was problematic with river temperatures (Figure 12) and Bay-Delta temperatures (Figure 6, 8, and 10) being too high. The February releases were prone to being drawn into the south Delta and exposed to salvage through April (Figure 13). A similar problem occurred in 2018.6 Flow pulses or trucking/barging may help resolve this problem.

One very encouraging development was the return of 200 spring-run adults to the San Joaquin River near Fresno, including unmarked fish that were apparently born in the river (not hatchery-born) and successfully navigated the river from near Fresno out the Golden Gate.

Figure 11. Summary of San Joaquin River Hatchery releases in 2019.

Figure 12. Water temperature and flow in lower San Joaquin River at Vernalis in winter-spring 2019.

Figure 13. Spring-run hatchery smolt salvage at south Delta export facilities in 2019.

Federal Sacramento River Livingston-Stone Winter-Run Recovery Hatchery

The Livingston Stone Hatchery near Redding released 408,000 winter-run salmon smolts to the Sacramento River and Battle Creek in winter 2019 (Figure 14). Smolts were released under favorable conditions. Salvage of these smolts at south Delta export facilities (Figure 15) indicates some degree of risk probably from being diverted to the south Delta via Georgiana Slough.

Figure 14. Summary of Livingston-Stone Sacramento River Hatchery releases in 2019.

Figure 15. Salvage of hatchery winter-run sized smolts at south Delta export facilities in 2019. Collection includes some late-fall-run hatchery smolts from the Coleman Hatchery.

In Summary

Hatchery salmon releases in wet year 2019 were generally made under favorable survival conditions. However, some releases were made under unfavorable conditions that were avoidable either by altering release timing or location, or by providing pulsed flows to support smolt migrations. Note that it will be several years before we see the adult returns from these tagged hatchery smolts. However, based on past experience,7 the portion of fish that were released in 2019 under unfavorable conditions will likely have poor adult returns.