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).

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

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.

Fall X2 should extend through December

In a recent post, I described the Fall X2 provision in the 2008 Delta Smelt Biological Opinion that protects smelt by requiring a modest Delta outflow from mid-August through October in Above Normal and Wet years.  In the same post, I described how the 2019 Biological Opinion for smelt would move the compliance point for Fall X2 upstream into the Delta, reducing low salinity zone habitat.   In this post, I suggest that the Fall X2 requirement should not only be retained with the old compliance point, but also that the applicable time period should extend through December.

First, if the X2 provision is not extended into December, this is what happens:  (1) Delta outflow drops to zero or even negative, as occurred this past November 2019 (Figure 1); and (2) the low salinity zone moves up into the Delta via the San Joaquin River channel toward the export pumps (Figure 2).

Second, winter-run salmon smolts that pour into the Delta from the Sacramento River in November and December of all but the driest years (Figure 3) will have difficulty surviving and exiting the Delta for the Bay and ocean.

Third, what few Delta smelt that may be surviving will be put at risk of being drawn into the central and south Delta (Figures 4 and 5).

Fourth, longfin smelt will be at risk to being drawn into the Delta (Figures 6 and 7).

Fifth, the primary food of young Delta native fishes, calanoid copepod adults, which concentrate in the low salinity zone, would be drawn into Delta (Figure 8).  Bay-Delta pelagic plankton productivity would suffer.

In conclusion, there are presently few constraints on water project operations in the Delta in November-December.  Freshwater outflow to the Bay can be zero or even negative, as occurred this past month, November 2019.  The updates to the Bay-Delta Water Quality Control Plan and to state permits that regulate Delta exports should extend Fall X2 through December in order to protect Delta native fishes.  Compliance would entail Delta outflows in the 8000-10,000 cfs range and/or Jersey Point salinity of about 500 EC.

Figure 1. Tidally filtered flow in the Sacramento River channel at Rio Vista and Jersey Point in the San Joaquin channel in November 2019.

Figure 2. Salinity (EC) at Jersey Point in the San Joaquin channel of the west Delta in November 2019.

Figure 3. Cumulative catch of winter-run Chinook salmon at Knights Landing rotary screw traps in fall-winter of water year 2017. Source: DOSS 2017.

Figure 4. Trawl catch distribution of Delta smelt fall 2011, the last time Delta smelt were relatively common.

Figure 5. Salvage of Delta smelt pre-spawn adults in fall-winter of water year 2003.

Figure 6. Longfin smelt trawl catch distribution in November 2011.

Figure 7. Longfin smelt trawl catch distribution in December 2011.

Figure 8. Adult calanoid copepod catch distribution in November 2011 zooplankton survey.

Failure to Protect Winter-Run Salmon in Fall 2019

In a December 2018 post, I focused on the importance of fall pulse flows in moving winter-run salmon juveniles downstream in the Sacramento River to the Delta and Bay. Without pulse flows, the juvenile winter-run are less likely to make or survive the downstream move from spawning and early rearing areas in the upper river. They are thus less likely to reach the ocean and contribute to subsequent recruitment into the adult population.

A gradual recovery of adult spawners, egg production, and wild fry production (Figure 1) has been helping recovery of the winter-run population since the population crash during the 2012-2015 drought. Wild fry production as estimated from Red Bluff screw trap collections is up sharply in 2019 (Figure 2 top chart).

However, in fall 2019, winter-run fry have received even less support in terms of river flow in their important journey to and through the Bay-Delta than in previous years. Numbers caught in lower river screw traps are very low (Figure 2 bottom chart), reflecting low movement rates from the upper river and poor survival. Both factors are a consequence of poor river flows. There are simply no reasons for Reclamation to be so stingy with Shasta Reservoir releases this fall, after a very wet year in 2019 and with Shasta Reservoir at or near a record-high level for this time of year.

A close-up of the Figure 2 data in Figure 3 shows some effort on the part of Reclamation to provide flow pulses,1 but the effort was not enough. Furthermore, Reclamation subsequently offset its meager augmentation by cutting reservoir releases in November (Figure 4). The November reduction further compromised the emigration and survival of juvenile winter-run salmon. Reclamation’s tendency to cut releases in fall and winter, the period when winter-run most depend on river flows, is pronounced in all but the wettest years (2011 and 2017) over the past decade (Figure 5). Such tendency probably has been deemed acceptable because downstream tributary flows (Battle Creek, Cow Creek, etc.) provide fall flow pulses in some years (e.g., fall 2016 Figure 6, fall 2011 Figure 7). But inflow pulses from those tributaries are downstream of the Redding spawning reach; in the spawning reach, flows come almost exclusively from Shasta Reservoir releases.

What is needed are modest flow pulses from Shasta Reservoir in fall, especially when pulses in downstream tributaries occur. Releases for several days in the 10,000-15,000 cfs range, or of slightly less magnitude when coincident with tributary flow pulses, would help emigration (and survival) of winter-run juvenile salmon from the upper river. Such pulses should not be followed by offsetting flow decreases, as have occurred this fall (Figures 3 and 4). Low flows following fall pulses cause redd dewatering or fry stranding of spring-run, fall-run, and late-fall-run salmon, which spawn in the upper river later in the season than winter-run.

The late November 2019, Thanksgiving week storm should provide ample Shasta storage and tributary flows to allow modest flow pulses from Shasta Reservoir. Such flow pulses would benefit all four salmon runs in the Sacramento River.

Figure 1. Emigration timing of juvenile winter-run salmon from the upper Sacramento River and the estimated number of juvenile salmon (millions) passing Red Bluff during water years 2004-2018. Note the poor production in critically dry 2014 and 2015 from loss of cold-water pool and associated catastrophic egg mortality.

Figure 1. Emigration timing of juvenile winter-run salmon from the upper Sacramento River and the estimated number of juvenile salmon (millions) passing Red Bluff during water years 2004-2018. Note the poor production in critically dry 2014 and 2015 from loss of cold-water pool and associated catastrophic egg mortality.

Figure 2. Daily estimated juvenile winter-run salmon catch per trap day passing Red Bluff in the upper river and Tisdale Weir in the lower river in summer-fall 2019. The numbers passing Red Bluff are strong, especially when one considers that they were the offspring of poor brood-year 2016.  

Figure 2. Daily estimated juvenile winter-run salmon catch per trap day passing Red Bluff in the upper river and Tisdale Weir in the lower river in summer-fall 2019. The numbers passing Red Bluff are strong, especially when one considers that they were the offspring of poor brood-year 2016.

Figure 3. Daily estimated juvenile winter-run salmon passage per trap day at Red Bluff in the upper river, also showing river flow in summer and fall 2019.

Figure 3. Daily estimated juvenile winter-run salmon passage per trap day at Red Bluff in the upper river, also showing river flow in summer and fall 2019.

Figure 4. Shasta/Keswick Dam releases in fall 2019, along with daily median flow average for 55 years.

Figure 5. Shasta/Keswick Dam daily average releases from 2009-2019, along with daily median flow average for 55 years.

Figure 6. Daily estimated juvenile winter-run salmon passage per trap day passing Red Bluff in the upper river and Tisdale Weir in the lower river in fall 2016. Note that the flow pulses (and associated higher catches) in early and late November were from tributary storm-related inflows. Such events had not occurred as yet in 2019 (Figure2).

Figure 7. Daily estimated juvenile winter-run salmon passage per trap day passing Red Bluff in the upper river and Tisdale Weir in the lower river in fall 2010. Note the flow pulses (and associated higher catches) in late October and in December.

 

 

 

  1. Reclamation’s sporadic 2000 cfs flow pulses in late October observable in Figures 2 and 3 were likely part of Reclamation’s contribution to maintaining Delta inflow and outflow for the Fall X2 requirement.