It is that time of year again for another Sacramento River Temperature Management Plan.  You know, the plan adopted to protect Sacramento River salmon from the operation of the Shasta/Trinity Division of the federal Central Valley Project of US Department of Interior, Bureau of Reclamation (Reclamation).  Past plans have failed to protect salmon since they became a requirement in 1990 in the State Water Board’s Water Rights Order 90-05.

The plans have failed even in wet years, including this wet year (four wet years have occurred since 2010).  This year, Shasta Reservoir is full, and there is more than ample cold water to deliver to the salmon below Shasta Dam (a “Tier 1” wet year).  Oroville and Folsom reservoirs are also full this year and ready to help Shasta supply the needs of salmon in the Sacramento River and Bay-Delta.

In this year’s 2023-sacramento-river-temperature-management-plan, Reclamation has committed to providing 53.5^oF water in the upper ten river miles (RM) of the Sacramento River downstream of Keswick Dam (RMs 290-300).  53.5ºF is the upper optimal threshold water temperature for adult salmon spawning, egg incubation, and fry emergence.  Reclamation has not always met this temperature in past wet years (Figure 1).

Other important benchmarks are maintaining lower Sacramento River water temperatures at and upstream of Red Bluff (RM 240) at <56^oF and at <68^oF downstream of Red Bluff (RMs 100-240).  Reclamation has exceeded these temperatures in the three most recent wet years (Figure 2).  Reclamation has not met summer water temperatures in the lower Sacramento River below 56^oF at Red Bluff (RM 240) and below 68^oF at Wilkins Slough (RM 120), because water diversions leave flows too low in summer (Figure 3).  In fact, Reclamation has given up trying to meet those temperatures.  The 2023 TMP evaluates maintaining 56^oF at Balls Ferry, 36 miles upstream of Red Bluff, but concludes, without any supporting data or evidence, that maintaining that objective would be too uncertain and risky.

Analyses of flow and water temperature data for Wilkins Slough indicates it generally takes 6,000 to 10,000 cfs flow at Wilkins Slough to maintain water temperatures below 68^oF in June, depending on air temperatures.  Note the water temperature in early June 2023 reached above 68^oF (Figure 2) as flows fell below 10,000 cfs (Figure 3).

Table 1 shows optimal temperatures for adult migration, holding, and spawning.  Adult salmon migrating, holding, or spawning are stressed by water temperatures above 60^oF.  Water temperature above 68^oF are considered “lethal” for migrating salmon – such temperatures occurred in June of three wet years (Figure 2).  Stressful water temperatures occurred during the spring in the lower Sacramento River in all four wet years (Figure 3).  Spawning and egg incubation water temperatures exceeded the target 53^oF for spring-summer spawning winter run salmon in all four wet years (Figure 1).

The 2023 Sacramento River Temperature Management Plan

“Significant uncertainties exist within the forecast that will require intensive real-time operations management throughout the summer to achieve the various goals and targets throughout the system.” (2023 TMP, p. 3) 

Comment:  Reclamation’s repeated strategy of staying close to 56º in a limited stretch of the Sacramento River, even in a year like 2023 when there is really no reason to adopt such a conservative strategy, unnecessarily compromises the salmon and sets a course for failure to meet permit requirements.  At the beginning of June, there were still endangered adult winter-run and spring-run salmon migrating up the lower Sacramento River.

As in 2023, Reclamation made overt decisions in 2017 and 2019 to drop flows below 7000 cfs in the lower reaches of the lower Sacramento River, knowing water temperatures would exceed their permitted upper limit and water quality standard of 68^oF.  Flows closer to Keswick Dam in Redding also dropped, allowing Red Bluff water temperatures to exceed their limit of 56^oF.

“The strategy of meeting 53.5 at CCR will likely result in average daily temperatures at or near 56 degrees F at BSF. Reclamation does not propose to operate the TCD explicitly to meet 56 degrees F at BSF under conditions that may require changes to TCD operations that could risk cold water pool resources for use later in the temperature management season. This would cause an unreasonable risk to other goals and objectives”.  (2023 TMP, p. 4)

Comment:  The TMP acknowledges from the start that Reclamation has no intention of meeting the 56^oF standard at Balls Ferry (RM 276), let alone Red Bluff (RM 240).  With CCR maintained at 53^oF, it takes more dam releases to keep the 60-mile upper river reach below 56^oF and the 100+ miles of lower river below 68^oF.  The 2023 Plan thus plainly ignores these other license and water quality standard requirements important to salmon survival.  Lower river water temperatures above 68^oF through late summer will also compromise the fall-run salmon migration up the river.

Update

Water temperatures in the Sacramento River downstream of Red Bluff steadily increased through June (Figure 4).  In over 100 miles of the Sacramento River from Red Bluff downstream to the mouth of the Feather River, Reclamation is operating in violation of federal/state water quality standards, the federal/state Endangered Species Acts, and state water rights permits.  Water temperatures have reached lethal levels for migrating adult and juvenile salmon blocking their migrations up and down the river, respectively.  Stress, disease, and predation are compromising two brood years of salmon production in a wet year!  Water diversions from the river below Red Bluff are approaching 6000 cfs (Figure 5) not counting diversions upstream or from tributaries.

In Conclusion

In conclusion, the Sacramento River Temperature Management Plan should cover all of Reclamation’s obligations under its permits and all applicable water quality standards, not just water temperatures in the upper 10 river miles of over 200 river miles used by salmon.

Table 1. Water temperature objectives for adult Central Valley salmon. (Sources: San Joaquin River Recovery Plan). Note that the temperatures cited in this figure are the maximum daily temperatures. The 2023 TMP target for winter-run Chinook spawning is an average daily temperature of 53.5ºF.

Figure 1, Water temperature (daily average) at the Clear Creek gage in the Sacramento River above the mouth of Clear Creek (RM 290) in wet years 2011, 2017, 2019, and 2023.

Figure 2. Water temperature (daily average) at the Red Bluff (RM 240) and Wilkins Slough (RM 120) gages in the Sacramento River in wet years 2011, 2017, 2019, and 2023.

Figure 3. Lower Sacramento River flow at the Wilkins Slough gage (RM 120) in wet years 2011, 2017, 2019, and 2023.

Figure 4. Water temperature and streamflow at Bend Bridge (RM 250) and Wilkins Slough (RM 120) in May-June 2023. Note 68^oF water quality standard and critical water temperature for salmon is exceeded.in late June at Wilkins Slough gage. The 56^oF standard was exceeded at Bend Bridge for much of May and June.

Figure 5. Streamflow at various gages in the Sacramento River from Keswick Dam (RM 300), Bend Bridge (RM 250) downstream to Wilkins Slough (RM 120) in May-June 2023. Note: tributary inflows in the reach below Bend gage in mid-June were approximately 5000 cfs in mid-May. Keswick Dam releases were increased in late June to maintain deliveries and sustain 5000 cfs at Wilkins Slough gage.

When I last assessed the status of the fall-run salmon population of the Yuba River near Marysville in a 1/31/22 post, I stated: “The population remains in a very poor state – at about 10% of recent historical levels during and subsequent to multiyear droughts 2007-2009 and 2013-2015 (Figure 1).” Since the record low run in 2017, the fall run on the Yuba River has not recovered.

The failure of the four more recent runs to show signs of recovery (Figure 1) is especially concerning because 2017 and 2019 were wet years. The failure to recover may be simply the lingering effects of the drought years 2014-2015 and the ongoing effects of the 2021-2022 drought. More likely, the spawning stock has collapsed and is in dire need of support. The 2022 run appears to be even worse than the past four runs,¹ thus adding to the concern.

This post delves into the many possible causes of, or contributors to, the collapse of the Yuba River fall-run salmon population. The story is a complicated one. It starts with broodyear 2014.

Figure 1. Yuba River fall-run salmon spawning escapement estimates 1953-2021. (Data source: GrandTab)

The first stop in pursuit of the potential causes of the recruitment failure that has occurred not only on the Yuba River, but in most of the other Central Valley fall-run salmon populations, is a close look at the escapement data.  The spawner-recruitment relationship (S/R) shown in the escapement data (Figure 2) provides a closer perspective than the simple histogram of the run sizes (Figure 1).

The S/R figure is a plot of the log of the escapement with the log of the escapement three years earlier. This is because about 80-90% of spawners are three years old.  The three red lines in Figure 2 show that adult spawners in 2014 produced the spawners 2017, which in turn produced the spawners in 2020.  The adult spawners in 2018 produced the spawners in 2021.  Spawners in 2019 produced spawners in 2022, which based on the incidental reports will likely show up to the lower left of 19.  The lower-left quadrant of an S/R plot is usually a place where a salmon population is headed toward collapse and an inability to sustain itself.

Figure 2. Yuba River fall-run salmon spawner-recruit relationship (1978-2021) with recruit number shown in chart for specific years. Red lines point from spawner to recruit year. For example, recruits in 2017 led to recruits in 2020. Recruits in 2014 (12,000) led to only 1500 in 2017.

When Yuba River escapement (recruitment) is adjusted for strays from other rivers, the recruitment level in record low 2017 (Figure 3) shows itself to be even more dire.  The Yuba River receives many strays because it carries a strong cold-water signal into the Feather River and on into the lower Sacramento River in late summer and early fall.  The Yuba River also attracts spring-run and late-fall-run hatchery salmon that are included in the Yuba River’s fall-run spawning counts.

It is helpful to start the analysis of the 2017 population crash by reviewing the early life cycle of broodyear 2014 – as eggs in their mothers.  Their parental stock, broodyear 2011, had been reasonably normal, if not in the range that might be considered the Maximum Sustained Yield 10,000-15,000 (Figures 1 and 2).  The strong numbers of broodyear 2011 spawners (and their broodyear 2014 eggs) arrived in the Bay in summer 2014.  The questions become what happened to:

1. those broodyear 2011 adult females;
2. their broodyear 2014 eggs and their hatchlings in summer-fall 2014;
3. the surviving broodyear 2014 fry in winter 2015; and smolts in spring 2015;
4. the yearlings, two-year-olds and three-year-olds in the ocean; and finally
5. the adults making up the 2017 run counted in the Yuba River spawning grounds.

The answer is that survival conditions were not good for all five categories above.  Each question is addressed below.

Figure 3. Yuba River escapement numbers. Source: PFMC 22, p.49.

1. The first question addresses the conditions that faced broodyear 2014 eggs when they entered the Golden Gate inside their broodyear 2011 mothers that fateful summer of 2014. Water-year 2014 was a critical drought year, during which the State Board weakened Delta water quality standards for the year.

• • Unusually warm water met the salmon when they entered the Bay in summer of drought year 2014 (Figure 4). By the time they reached the mouth of the Feather River at Verona (if they got that far), water temperatures were near the lethal 75º F level through September (Figure 5).  Elevated water temperatures occurred through the entire route from the Golden Gate to the Yuba River.
  • Once on the spawning grounds of the, Yuba the parents of broodyear 2014 eggs encountered drought-year low flows (Figure 6), which in addition to being warm provided minimal available spawning habitat quantity and quality.
  • By the time the parents were ready to spawn in early fall, they were likely compromised by disease and thiamine deficiency, limiting the viability and survival of the broodyear 2014 eggs, and thereby the potential reproductive success of broodyear 2014 and its contribution toward 2017 recruitment.

2. The second question addresses the subsequent fate of surviving broodyear 2014 eggs and the hatched alevins in gravel redds. The eggs and alevins in the spawning beds faced unusual stresses in the form of erratic flow and very low flows (Figure 7).  Eggs spawned in October-November were subjected to scouring flows in December.  Eggs spawned in December under the high flows were subsequently subject to dewatering in January.

Figure 4. Water temperature in San Francisco Bay spring-summer 2014.

Figure 5. Water temperature in Sacramento River below mouth of the Feather River at Verona gage July-October 2014.

Figure 6. Streamflow in Yuba River at Smartsville and Marysville gages July-October 2014.

Figure 7. Yuba River streamflow in water year 2015 and 53-year average at Marysville gage.

3. The third question addresses conditions in the late fall through spring in critical drought water year 2015. Emergent fry likely benefitted from the February flow pulse that facilitated some fry movement out of the Yuba toward the Delta (see Figure 7).  Those fry that did not move were then subjected to extremely low flows (and stressful water temperatures) through the spring in the lower Yuba River and the lower Sacramento River below the mouth of the Feather River (Figure 8).  Delta and then Bay conditions were at their worst for young Yuba salmon on their way to the ocean in the spring of drought year 2015, made worse by the State Board’s continued weakening of water quality standards.

Figure 8. Streamflow and water temperature in the lower Sacramento River below the mouth of the Feather River at Verona gage in winter-spring 2015.

4. The fourth question regarding broodyear 2014 addresses growth in the ocean from 2015 through early summer 2017. In the ocean, they were subjected to strong fishery pressure (Figure 9) in all three years by the commercial and sport fisheries.  This provokes a series of questions.  Why did the Pacific Fisheries Management Council or PFMC allow those 50%+ harvests after the 2008-2009 collapse and fishery closures, and lack of subsequent population recovery?  Had the fall-run salmon populations really recovered sufficiently to sustain 50%+ harvests?  How accurate were those harvest rate estimates?  How hard were the stocks being preyed upon by seals and orcas?  Were the salmon whose diet had largely consisted only of anchovies becoming thiamine deficient by the time they spawned in the Yuba in early fall 2017.  In considering all these questions, one can only conclude that the summer upstream migration of fall-run salmon to the Yuba in 2017 had been highly compromised before it started.

5. The fifth and final question regarding broodyear 2014 salmon addresses conditions adult fish faced when they re-entered fresh to spawn after having been subjected to high harvest rates in the ocean from 2015-2017 (implied in Figure 9).  Upon returning to the Bay in summer 2017, a wet year, they encountered much better conditions during their upstream migration and spawning period.  After a final tweak by the summer river fishery, they spawned in the Yuba River in record low numbers.

Nearly identical circumstances and outcomes occurred with broodyear 2015 in 2018 (see Figure 3).  Broodyears 2016-2019 were subject to similar stresses.  Broodyears 2020 and 2021 were subject in-river to critical drought years 2021 and 2022.

In conclusion, it appears that the damage to broodyear 2014 and broodyear 2015 had been done for the most part by the time they returned as adults to the Bay in 2017 and 2018.  The record-low numbers of spawners estimated from the carcass surveys in 2017 and 2018 (Figure 1 and 2) were the cumulative effect of a series of survival factors, beginning with stresses on their parents in drought years 2014 and 2015, and ending with high harvest rates in the ocean and rivers in 2017 and 2018.  Management decisions by the State Board and PFMC, with acquiescence by federal and state resources agencies, contributed to this fateful series of events.  The events and their consequences were predictable, and the State Board and PFMC should have anticipated them and taken appropriate measures at the time.

It appears the same mistakes were made in regard to broodyears 2016-2021.  The effects of drought in years 2021 and 2022 will likely contribute further to the crash of the Yuba River salmon population, with even lower Yuba River and Central Valley salmon escapement in 2023-2025.

For more on the problems faced by Yuba River fall-run salmon and what can be done about them, see this October 2018 post.

Figure 9. Sacramento River fall-run salmon index 1983-2019. The 122 on y-axis is the target starting population level (122,000) under which harvest is allowed. Note the fisheries were closed in 2008 and 2009. Source: PFMC.

Following some improvement in the numbers of adult fall-run Chinook salmon returning to spawn in the Stanislaus River and the Merced River from 2012-2017, overall escapement in 2020 and 2021 to San Joaquin River tributaries was severely depressed.  Better flows and water temperatures could help reverse this decline.

In February 2017, I wrote about the fall Chinook salmon runs on the San Joaquin River’s three major tributaries over the previous six years.  Salmon counts in San Joaquin tributaries showed an increase in returning adults in the 2012-2015 drought compared to the poor returns in 2007-2009 drought (see Figures 1 and 2).   The numbers of spawners in 2012-2015 were still well below the returns in the eighties and nineties that corresponded to wet water year sequences, but the increase seemed to suggest progress.

In a December 2019 update, I  updated the earlier post with numbers from the 2016-2018 runs. The 2016 and 2017 runs were the product of poor rearing conditions in 2014 and 2015, both critical drought years, but with good fall adult migration conditions.  The 2018 run was a product of normal-water-year rearing (2016), but poor adult migrating conditions.  The 2016 and 2017 runs were strong in the Stanislaus and Merced rivers (see Figure 3), with both rivers benefitting from hatchery production and strays.  The markedly smaller runs in the Tuolumne (typical throughout the last decade) also benefitted from hatchery strays (Figure 4).  One strong component of the strays was the unusually high proportion of strays from the upper Sacramento River’s Battle Creek hatchery, whose managers’ strategy during the 2014-2015 drought was to truck their fall-run salmon smolts to the Bay, a practice that causes high straying rates, including to the San Joaquin tributary runs.

The 2018 San Joaquin run was lower, but still an improvement over the drought-influenced runs in 2007-2011 (Figure 2).  Spring rearing conditions in 2016 and fall adult migration conditions in 2018 were generally better than they were during the critical drought years, although still stressful.  Also, most of the Mokelumne and Merced hatchery smolts were released to the Bay and west Delta, respectively, in 2016, a likely positive factor in contributing strays to overall escapement.  A further explanation for this improvement was better hydrology-related habitat and migration conditions prescribed in the 2008-09 federal biological opinions that generally led to improved habitat conditions.

In the three years (2019-2021) since 2018, runs generally declined (Figure 3) despite being the product of two wet (2017 and 2019) and one normal (2018) year.  One reason for the reductions was that there were fewer strays from hatcheries. For example, the Merced hatchery smolt releases in 2017 were at the hatchery instead of in the Bay, and thus had poor returns.  Battle Creek hatchery returns were also lower, with less straying by smolts released near the hatchery.

The poor returns in 2020 in all three rivers are especially troubling, given they are the product of a good wet year run (2017) and reasonable rearing conditions in winter and spring of normal year 2018.  One factor in the San Joaquin watershed in late summer and early fall 2020 was unusually low flows and high water temperatures for a normal water year (Figures 5 and 6).  Based on the high number of returns of 2018 Merced hatchery smolt releases straying to other rivers (Figure 7), it appears that a compounding factor to these low flows and high water temperatures was high rates of straying by salmon sourced in San Joaquin watershed to the Mokelumne, American, and Feather Rivers.

The relatively high proportion of the Stanislaus River escapement in the 2021 San Joaquin run appears to be a result of attraction to the Stanislaus from a very warm lower San Joaquin River (Figure 8).  The Stanislaus is the first cool tributary encountered by salmon on their journey up the warm San Joaquin in late summer and early fall.

In summary, there is much straying to and from the San Joaquin salmon spawning tributaries.  Adult run size (escapement) is a function of straying, winter-spring flows and water temperature in the San Joaquin and its tributaries during the winter-spring rearing season, and streamflows and water temperatures during the annual late summer and fall spawning run.  The release locations of smolts from the Merced River hatchery and other hatcheries also plays a role.

Salmon runs to the San Joaquin and its tributaries could be improved with better streamflow and water temperature management.

Figure 1. Fall run salmon escapement to San Joaquin River and tributaries 1989-2021. Source: Grandtab.

Figure 2. Plot of 1975-2021 fall run salmon escapement to San Joaquin River tributaries. Data source: GrandTab.

Figure 3. Plot of 2015-2021 fall run salmon escapement to the San Joaquin River tributaries. Data source: GrandTab.

Figure 4. Returns of code-wire-tagged (cwt) salmon to Tuolumne River in 2016-2017 from five Central Valley hatcheries. Source: cwt return data in https://www.rmpc.org.

Figure 5. July-December water temperature in San Joaquin River at Vernalis in 2020, and historical average.

Figure 6. July-December streamflow in San Joaquin River at Vernalis in 2020, and historical average.

Figure 7. Adult spawner returns to four hatcheries and spawning grounds in 2020 of 2018 Merced Hatchery tagged smolts released in Bay. (Note there were no records for Battle Creek returns.)
Source: cwt return data in https://www.rmpc.org.

Figure 8. Water temperatures in the lower San Joaquin River at Vernalis (VNS), Brant Bridge (BDT), and Mud Slough (MSG), and Ripon (RIP) on the lower Stanislaus River in September 2020. Note adult salmon generally avoid 72°F water.