Category Archives: Bay-Delta

Warm Water Temperature in lower Sacramento River in May 2024 Migrating Adult and Juvenile Salmon and Sturgeon Are Compromised in Spring of an Above Normal Year Following a Wet Year

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In the third week of May 2024, the water temperatures in the lower Sacramento River recorded at Wilkins Slough increased to 72oF, well above the 68oF water quality standard (Figure 1). These warm water temperatures occurred in a wet spring of an Above Normal water year that is following a Wet water year.

The water temperature spike occurred between prescribed pulse flow releases from Shasta Dam in May (Figure 1).  Three pulse flows were prescribed this spring to promote and assist migration of juvenile salmon into the lower Sacramento River and the Delta.

After the second pulse in early May, the lower river flow was allowed to drop to a drought-level 5000 cfs, causing the high water temperatures.  Shasta Reservoir was virtually full at 4.3 MAF during all of May.

The Central Valley Basin Plan’s water quality objective for the lower Sacramento River is 68oF maximum “during periods when temperature increases will be detrimental to the fishery.” (P. 3-14).  Declining tributary inflows and increased mainstem water diversions contributed to the low flows.  Cooler American River and Feather River inflows to the Sacramento River below Wilkins Slough have kept north Delta water temperatures in the Sacramento River channel at Freeport and Rio Vista cooler at 64-67oF (Figure 2).

Many juvenile salmon emigrate to and through the Delta in spring (Figures 3-5).  High water temperatures in the lower Sacramento River lead to a drop-off in migration and increase in stress and predation, ultimately reducing survival and the numbers of smolts reaching the ocean.  Many spring-run and fall-run salmon smolts stay in the Delta through June and into July (Figures 6 and 7).  A majority of these smolts are wild salmon adapted to emigrate with the late spring snowmelt season; they rear in the Delta prior to entering the ocean.

Adult spring-run and winter-run salmon also migrate upstream through the Bay-Delta to upriver spawning areas in the spring.  They too benefit from the pulse flows, but also suffer stress from the high water temperatures on the journey upstream.  Adult Chinook salmon avoid migration through water whose temperature is at or above 72oF.

Green and white sturgeon also spawn in the spring in the lower Sacramento River from Red Bluff downstream to Verona (river miles 200 to 100).  Optimal water temperatures for spawning and early rearing are 50-65oF.  Water temperatures above 65oF are stressful and lead to poor survival.  Pulse flows stimulate spawning.  Peak water temperatures of 68-72oF in mid-May are considered detrimental to juveniles and adults, as well as lethal to sturgeon eggs and embryos.

The river conditions described above for mid-May 2024 are typical in drought years, but not in wet years.  The pulse flow certainly helps in the salmon and sturgeon migrations.  But lower Sacramento River base flows should not be allowed to fall below the 8,000-10,000 cfs needed to maintain water temperatures at or below 65oF to protect migrating adult and juvenile salmon and sturgeon.

Wet-year recoveries are essential given how poor conditions are in drought years.  The 2020-2022 drought led directly to the complete closure of salmon fisheries in 2023 and 2024 and more stringent requirements for the white sturgeon fishery in 2024.

Good migration conditions must be maintained in Wet years, including sequences of Wet and Above Normal water years, if there is to be any recovery from the multiyear droughts.

Figure 1. Daily-average Sacramento River flow and water temperature at Keswick Dam (RM 300) and Wilkins Slough (RM 120) in spring 2024. Note water temperature at Wilkins Slough (purple line) has exceeded the water quality standard of 68oF for the lower Sacramento River. Afternoon water temperatures on May 15 reached 72oF. Note the three pulse flows conducted by Reclamation (blue line) to support salmon migration helped to lower water temperatures. Note the sharp rise in water temperature in mid-May at Wilkins Slough after cessation of the second prescribed pulse flow, when streamflow dropped below pre-pulse flows.

Figure 2. Daily-average Sacramento River flow at Freeport (blue line) and water temperature a Freeport (green line) and Rio Vista (orange line) in spring 2024.

Figure 3. Rotary screw trap capture rate of juvenile salmon in 2024. Also shown is river flow rate and water temperature and turbidity.

Figure 4. Trawl Catch Index of juvenile salmon near Sacramento in the Sacramento River in Water Year 2024. Also shown is river flow rate and water temperature and turbidity.

Figure 5. Trawl Catch Index of juvenile salmon near Chipps Island in the eastern Suisun Bay in Water Year 2024. Also shown is river flow rate and water temperature and turbidity.

Figure 6. Salvage of juvenile salmon in water year 2023 at south Delta export pumping plants. Also shown are tagged hatchery salmon smolt collections by hatchery release groups and run type, and Delta flow and export rates.

Figure 7. Salvage of juvenile salmon in water year 2024 at south Delta export pumping plants. Also shown are tagged hatchery salmon smolt collections by hatchery release groups and run type, and Delta flow and export rates. Wild fry and smolt groups are noted; they can be segregated given the general lack of tagged hatchery smolts for the size group and time period.

Trucking Central Valley Salmon Smolts from Hatcheries to Salt Water

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A November 1, 2023 article, originally published in High Country News and later posted in Maven’s Notebook, describes the practice of trucking juvenile salmon from hatcheries for release in salt water as a “culprit,” stating: 

According to a growing body of scientific evidence, it’s also the reason that many salmon are getting lost on their way back to their birth rivers, placing the future resilience of the species at risk…. These trucked hatchery fish may survive longer in the short term, but they will return to the river system years later with massive gaps in their memory and little sense of how to locate their spawning grounds. Instead, many end up wandering up unfamiliar rivers or streams and spawning far from home.

What the article doesn’t say is that juvenile salmon released directly in San Francisco Bay or San Pablo Bay, or in the ocean, are as much as ten to a hundred times more likely to live to spawn as are juvenile fish released near their hatcheries of origin.

It is true that trucked hatchery salmon smolts have a higher “straying” rate than smolts that are released near the hatcheries in which they were raised.  Sometimes, that difference in straying is quite dramatic.

On the other hand, while straying does cause salmon to wander into Central Valley rivers other than those from which they came, most of the rivers to which they stray would have few if any salmon at all if it were not for these strays.  And right now, trucking is necessary for the water projects to meet their mitigation goals of putting salmon back into the ocean to sustain salmon fisheries.

Furthermore, if it were not for trucking, the investment of hundreds of millions of dollars in salmon hatcheries would largely be for naught.  Only in wetter years do releases of hatchery-raised salmon near the hatcheries come anywhere close to achieving hatchery production goals.  In the drier years, when hatcheries provide their greatest benefit, very few fish released at or near the hatcheries survive downstream migration through Central Valley rivers and the Bay-Delta.

Trucking also reduces the competition between hatchery smolts and wild fish for limited habitat downstream of the Valley’s rim dams.

Below, I provide examples of straying rates for the Mokelumne Hatchery and Coleman Hatchery, from which some of the highest percentages of straying occurs.  The American and Feather River hatchery releases also have elevated straying of trucked smolts, but at much lower rates.

Mokelumne River Hatchery Straying

One of the greatest straying problems is from the Mokelumne Hatchery smolt releases, especially in drought years.  The Mokelumne Hatchery trucks more smolts percentage-wise than the other six salmon hatcheries.  However, coastal releases of Mokelumne Hatchery fish in drought years 2014 and 2015 yielded returns of 0.79-1.15% compared to 0.01% from the river release below the hatchery (Table 1).

However, straying rates for coast releases were greater than 50% to other rivers and hatcheries compared to 0% for the Mokelumne River releases (Figures 1-4).

Table 1.  Mokelumne Hatchery selected release groups – number and survival rates

 Coleman (Battle Creek) Hatchery Straying

Coleman Hatchery smolts trucked to the Bay have a much greater rate of straying than smolts released near the hatchery near the mouth of Battle Creek near Redding (Figures 5 and 6).  However, smolts released near the hatchery have a much lower survival/return rate (Table 2).

Table 2.  Coleman Hatchery selected release groups – number and survival rates.

Stray Counting

Other than showing up in these figures, strays are not accounted for in escapement estimates for individual rivers, and they are not counted in return tabulations of their hatchery of origin.  Fish counted at a hatchery or in river surveys simply get accounted for in the escapement estimate for the river to which they return.  As an example, tabulations for returns to the American River (Figure 7) show that in 2015, about a quarter of the tabulated escapement originally came as strays from the Mokelumne Hatchery.

Conclusion

It is good practice to reduce straying of hatchery salmon.  But in my view, arguments about straying often tend to obscure, not improve, the problems of poor survival of both wild and hatchery salmon in dry years due to inadequate flow and other aspects of poor water management.  And as long as commercial and sport salmon fisheries in California and Oregon are substantially dependent on hatchery production in the Central Valley, it makes a lot of sense to prioritize the survival to adulthood of hatchery salmon over their fidelity to natal rivers and streams.

For more on the trucking of juvenile hatchery production, see: https://calsport.org/fisheriesblog/?s=trucking&submit=Search

Figure 1. Returns from a Mokelumne Hatchery release to Golden Gate in 2014. Yellow dot is hatchery location. Green dot is release location.

Figure 2. Returns from Mokelumne Hatchery release to Santa Cruz Harbor in 2014.

Figure 3. Returns from Mokelumne Hatchery release to Moss Landing in Monterey Bay in 2015.

Figure 4. Returns from Mokelumne Hatchery release to lower Mokelumne River in 2014.

Figure 5. Coleman Hatchery 2014 smolt release group returns. Green dot is release site.

Figure 6. Coleman Hatchery 2014 smolt release group returns. Green dot is release site.

Figure 7. Green wedges are proportion of tags recovered in the American River in 2015 whose origin was the Mokelumne River Hatchery. Source: Pacific Fisheries Management Council.

Super Moon #4 – Harvest Moon (9/28/23)

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The Harvest Moon is the full moon nearest the autumn equinox (in 2023, the equinox was on 9/22).  The Harvest Moon greets fall-run salmon returning from the ocean to the Central Valley.  Unlike the previous two full moons, the 2023 Harvest Moon is coincident with improved conditions for fish.

The last two full moons, the Sturgeon Moon and the Blue Moon, wreaked havoc on the Bay by contributing to warm water and algae blooms (Figure 1) and to the associated low dissolved oxygen levels that led to sturgeon mortality in the Bay (Figures 2-4).  Low Delta water inflows and outflows contributed to the problems.1  The fish kills that occurred in the Bay were generally a consequence of poor water quality brought on by high summer water temperatures, associated algae blooms, and low dissolved oxygen levels (hypoxia).

Water temperatures above 20oC/68oF bring about stressful conditions, while those above 22oC/72oF lead to lethal conditions such as those that occurred in summer 2022 and summer 2023.  Other effects of warm water include plankton blooms and low dissolved oxygen levels that result from the algae die-offs after such blooms.  Though there is no direct evidence of the magnitude of mortality events, there is evidence that such events may have occurred in the Bay in summer 2022 and summer 2023.  Summer conditions in 2022 and 2023, and perhaps prior years, were likely major trauma incidents that had significant short-term and perhaps long-term effects on the sturgeon populations of the San Francisco Bay Estuary (Bay-Delta Estuary).

The warm water and algae blooms in the Bay abated early in September 2023.  Water quality improved with the advent of cooler air temperatures and with the higher Delta outflows (Figure 5) associated with the Fall X2 requirement from the Delta Smelt Biological Opinion (US Dept. of Interior).  The cooling of the water ensured that salmon could safely make their fall runs into the Central Valley rivers during the Harvest Moon, the last super moon of 2023.

Figure 1. River water stage (elevation) and water temperature at Rio Vista Bridge in Sacramento River channel of the Delta near exit to the Bay. Stage drops (draining of the Delta toward Bay) occurred prior to and after the four Super Moons of summer 2023. Note the warm water (74-75oF) draining from the Delta during the two mid-summer drain periods.

Graph of Water temperature (C), dissolved oxygen (DO, mg/l), and chlorophyll (mg/l) in western Suisun Bay in summer 2023.

Figure 2. Water temperature (C), dissolved oxygen (DO, mg/l), and chlorophyll (mg/l) in western Suisun Bay in summer 2023. Note algae bloom at end of July that began during the warm water period. Note very low DO (<6 mg/l) after bloom die-off in August.

Graph of Chlorophyll concentration (mg/l) in 2022 and 2023 in Suisun Bay.

Figure 3. Chlorophyll concentration (mg/l) in 2022 and 2023 in Suisun Bay. Note two summer algae blooms in red circles.

Graph of Dissolved oxygen concentration (mg/l) in 2022 and 2023 in Suisun Bay.

Figure 4. Dissolved oxygen concentration (mg/l) in 2022 and 2023 in Suisun Bay. Note low levels after two summer algae blooms in red circles.

Graph of Daily average flow in summer 2023 and 25-year average at Rio Vista in the lower Sacramento River channel of the Delta leading into Suisun Bay. Late August and September increases are related to the Fall X2 requirement of Delta water projects in wet years.

Figure 5. Daily average flow in summer 2023 and 25-year average at Rio Vista in the lower Sacramento River channel of the Delta leading into Suisun Bay. Late August and September increases are related to the Fall X2 requirement of Delta water projects in wet years.

Sturgeon Moon #3 – August 30 Blue Moon

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August 2023 has come to an end, following the second “Super Moon” of the month – a Blue Moon. The first full moon of the month was called a “Sturgeon Moon,” originally coined in reference to the ease of catching sturgeon in the Great Lakes during a full moon in summer. The cycle began with the quarter moon and neap tide on July 24 until the full moon on August 1.1

This year’s Super Moons have made a mess of San Francisco Bay, as they did in summer 2022. This year’s August moons have again, regrettably, led to a die-off of sturgeon and other Bay fish.2 The Super Moons’ strong tides caused warm water from the Delta to drain into the Bay, making the usually cool Bay unseasonably warm. (The ocean Blob may have added to some of this summer’s warm Bay water.) The warm water and the associated algal blooms (and their die-offs) have led to unprecedented low dissolved oxygen levels in the Bay, which can kill fish.

While the degree of harm has not been as bad as last year’s summer blooms that were aggravated by the 2022 drought, this year’s algal blooms have also harmed fish despite generally beneficial wet-year conditions. Last summer, there was die-off of nearly a thousand adult white sturgeon in the greater San Francisco Bay due to algal blooms. More dead white sturgeon adults also showed up on Bay beaches again this summer.3

The Bay turned warmer under this summer’s Super Moons than under those last summer (Figure 1). Blooms are still happening, as indicated by high turbidities and chlorophyll levels in portions of the Bay (Figures 1-3). The draining of warm Delta water to the Bay just before the 2023 Super Moons (Figures 4 and 5) warmed the Bay (Figure 6). Low dissolved oxygen continues to plague the Bay (Figure 6). The most recent bloom is depicted in Figures 7 and 8.

The summer 2023 Super Moons and their algal blooms make a complicated story, with the effects of various factors implicated in the blooms, and their role in fish die-offs in the Bay, yet to be fully determined. My concern centers on how warm the Delta becomes in summer before it drains into the Bay during the lunar tidal cycles (Figure 9). The lower rivers and Delta received too little flow from major Central Valley reservoirs for a wet year with full reservoirs. This is an increasing trend that deserves a lot more attention to ensure protection of the Bay’s fish and other public trust values. Otherwise, the trend will simply be chocked up to climate change.

Graph of North Bay (San Pablo Bay at Richmond Bridge) water temperature and turbidity in summer 2023.

Figure 1. North Bay (San Pablo Bay at Richmond Bridge) water temperature and turbidity in summer 2023. Note the presence of the three blooms indicated by high turbidity levels (>100 FNUs)

Graph of Chlorophyll levels at Martinez CA gage between East and North San Francisco Bay in summer 2023.

Figure 2. Chlorophyll levels at Martinez CA gage between East and North San Francisco Bay in summer 2023. Note three periods (green circles) of blooms located at this site.

Graph of Chlorophyll levels at Grizzly Bay gage (in northwest East Bay) in summer 2023.

Figure 3. Chlorophyll levels at Grizzly Bay gage (in northwest East Bay) in summer 2023.

Graph of Salinity (EC) at eastern Suisun Bay gage (in east Bay) in summer 2023.

Figure 4. Salinity (EC) at eastern Suisun Bay gage (in east Bay) in summer 2023. Red arrows indicate periods of draining prior to and between full moons.

Graph of Daily average (tidally filtered) discharge at Pittsburg gage in Suisun Bay summer 2023.

Figure 5. Daily average (tidally filtered) discharge at Pittsburg gage in Suisun Bay summer 2023. Red circles indicate drainage rates to Suisun Bay prior to two Super Moons (August 1 and 30).

Graph of Hourly dissolved oxygen levels in Grizzly Bay in summer 2023.

Figure 6. Hourly dissolved oxygen levels in Grizzly Bay in summer 2023. Note inverse relationship with chlorophyll levels in Figure 4. The low dissolved oxygen levels (<5 mg/l) began with the first bloom (August 1) and continued through August. Also note the Bay water quality standard is a minimum 6 mg/l dissolved oxygen level for fish health.

Satellite imagery of chlorophyll levels in San Francisco Bay on 8/29/2023.

Figure 7. Satellite imagery of chlorophyll levels in San Francisco Bay on 8/29/2023.

Graph of water temperature, chlorophyll, and salinity in Suisun Bay in summer 2023.

Figure 8. Water temperature, chlorophyll, and salinity in Suisun Bay in summer 2023. Note algal bloom in late August that began after the late-August draining of the Delta into the Bay when water temperatures reached 24oC (75oF).

Graph of San Francisco Bay water temperatures from 2007-2023.

Figure 9. San Francisco Bay water temperatures from 2007-2023. Note 2023 reached 70oF (see Figure 2) a recent record reached not even reached in critical drought years 2014, 2015, and 2022.

  1. Spring tides always happen when the Moon is at the full or new phase, which is when the Sun, Moon and Earth are in alignment. Neap tides occur around the first and last quarter phase of the Moon, when the Moon’s orbit around Earth brings it perpendicular to the Sun. ↩
  2. https://calsport.org/fisheriesblog/?p=4398 ↩
  3. https://www.sfchronicle.com/climate/article/fishkill-18279379.php ↩

Sturgeon Moon 2 – August 30

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In an August 9 post, I described the effects on San Francisco Bay and its sturgeon from the August 1 Sturgeon Moon.  I hypothesized that the draining of warm water from the Delta into the Bay over several days of the strong neap tide during the Sturgeon Moon caused an algae bloom and unseasonably warm water in the Bay (Figure 1) that was killing sturgeon, as it had in summer 2022.  I blamed the warm water on low river flows and high water diversions in the Central Valley that caused the Delta to reach 75oF and the Bay to subsequently reach an unprecedented 72-73oF.  The warm water, abundant sunshine, and generally high nutrients caused the bloom and the low dissolved oxygen levels that resulted in fish dying.

These events are about to reoccur with the August 30 Super Moon.  Once again, warm water will drain from the Delta on several days of strong neap tides the week before the Super Moon (probably around August 24).   The bloom should appear about August 28, about two days before the full moon.

The key question is how warm the Delta will be when it drains into the Bay.  This depends on air temperatures, river flows, and Delta outflow (the product of reservoir releases, Delta inflow, and water diversions).  With an expected general heat wave August 14-17, there is reason to be concerned that water draining from the Delta could be warm once again.

There have been several mitigating factors since the August 1 Super Moon.  Reservoir releases have increased slightly over the past month (Figure 2).  The strength of the spring and neap tides has decreased slightly following the August 1 full moon (Figure 2).  Higher Delta inflows (Freeport) have reduced Delta water temperatures slightly (Figure 3).

To minimize the strength of the potential bloom, warming, and fish die-off in the Bay, it is essential to keep Delta water temperatures down before the August 25-26 neap tide.  Several interdependent actions come to mind: (1) Increase lower Sacramento River flows over the next 10 days by several thousand cfs to get Wilkins Slough water temperatures down to about 68oF.  (2) Ensure that the extra Wilkins flow reaches the Delta at Freeport to keep Delta inflow up several thousand cfs.  (3) Increase Delta outflow during the August 22-24 spring tide by reducing south Delta exports, to minimize the build-up of warm water in the Delta prior to when the Delta drains to the Bay on the August 25-26 neap tide.

These actions will hopefully minimize the damage caused by Central Valley water management to the Bay ecosystem and specifically to the white sturgeon population during the next Super Moon cycle.

Satellite image

Figure 1. San Francisco Bay algae bloom on July 30, 2023. Source

Graphs showing Delta inflow (Freeport) and Delta outflow to Bay in week since the August 1 Super Moon.

Figure 2. Delta inflow (Freeport) and Delta outflow to Bay in week since the August 1 Super Moon. Note the spring tide has gotten slightly stronger and Delta inflows have increased (due to increased Folsom and Oroville reservoir releases)

Graph showing Delta inflow (tidally filtered and hourly) from the Sacramento River and water temperature at Freeport July-August 2023.

Figure 3. Delta inflow (tidally filtered and hourly) from the Sacramento River and water temperature at Freeport July-August 2023.

Graph showing Lower Sacramento River streamflow and water temperature at Wilkins Slough gage July-August 2023. Water temperature remains high (>20C, 68 F) under low streamflow.

Figure 4. Lower Sacramento River streamflow and water temperature at Wilkins Slough gage July-August 2023. Water temperature remains high (>20oC, 68oF) under low streamflow.