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.

Why is the Delta so Warm in Summer?

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72-75oF is too warm for native fishes in the Delta.  In drought years, we are not surprised when the Delta is too warm in summer, particularly when the State issues emergency drought orders that allow low Delta inflows and outflows.  But we do not expect the Delta to be warm in summer of wet years like the three latest 2017, 2019, and 2023 (Figures 1 and 2).  Water temperatures were not that warm back in wet year 2011 or in recent decades 1995-2004 (Emmaton) or 2001-2010 (Rio Vista) (Figures 1 and 2).

What is causing the high summer Delta water temperatures?  Part of the cause is low Sacramento River flows and associated high water temperatures coming into the Delta.  Available streamflow and temperature data in the Sacramento River just above and at the entrance to the Delta for Wilkins Slough, Verona, and Freeport (Figure 3) clearly show this pattern.  Summer flows in the lower Sacramento River at Wilkin Slough were particularly low in 2017 and 2023 (Figure 4), which led to higher Delta water temperatures (see Figures 1 and 2).  Summer 2011 was the only year after 2010 that met the water quality standard of 68oF water temperature (Figures 5 and 6).  Water temperatures at Wilkins Slough, Verona, and Freeport where the Sacramento River enters the Delta have the same consistent pattern (Figures 7 and 8) – water temperatures are too warm (>68oF) in summer.

It seems that the resource and water management agencies have simply written off the problem as purely a function of climate change/global warming.  They should not.

When Valley air temperatures are high (near average daily 80oF), it takes flows up to 8,000-10,000 cfs in the lower Sacramento River to keep water temperatures down near 68oF (Figures 9-11).  If lower Sacramento River flows at Wilkins Slough can be maintained at an average of about 8,000 cfs (range of 6,000-10,000 depending on air temperatures), the water temperature standard of 68oF (20oC) can more frequently be met (see Figure 4).  Also, Delta water temperatures can more frequently be maintained below 72oF.

If this had been accomplished in the years after 2011, then smelt and fall-run salmon population crashes may have been less severe.

Figure 1. Water temperatures (average daily) at Rio Vista in north Delta from June through August of wet years 2011, 2017, 2019, and 2023 along with average for decade of 2001-2010.

Figure 2. Water temperatures (average daily) at Emmaton in west Delta in June through August of wet years 2011, 2017, 2019, and 2023 along with average for decade of 1995-2004.

Figure 3. Three water temperature gage locations (in bold type) on the lower Sacramento River above and at the entrance to the Delta near Sacramento. Other gages also noted.

Figure 4. Stream flow (average daily) at Wilkins Slough in the lower Sacramento River upstream of the Delta in wet years 2011, 2017, 2019, and 2023 along with average for decade of 1995-2004. Note midsummer flows in 2023 and 2017 were only half the average of 1995-2004. Flows were higher in late summer in the four recent wet years to meet the Fall X2 requirement for wet years.

Figure 5. Water temperatures at Wilkins Slough in the lower Sacramento River in years 2008 to 2023 along with water quality standard (red line). The four warmest summers were critical drought years when water quality standards were relaxed because of limited available water supply.

Figure 6. Water temperature (hourly) at Wilkins Slough in the lower Sacramento River in summer 2011 with average daily for previous 14 years. The water quality standard is 68oF average daily temperature. The standard was met in 2011 and in many of the years before that.

Figure 7. Available water temperature data at Verona in the lower Sacramento River in years 2008 to 2016. Water year 2011 was the only wet year in the sequence of available data from the Verona gage.

Figure 8. Water temperature and river flow (average daily) in Sacramento River at Freeport in north Delta 2008-present.

Figure 8. Water temperature and river flow (average daily) in Sacramento River at Freeport in north Delta 2008-present.

Figure 9. Red Bluff air and water temperatures (average daily) with Wilkins Slough streamflow and water temperatures (average daily) in summer of wet year 2017. The 68ºF water temperature standard could not be met under the midsummer <6000 cfs level of flow. It took flows of nearly 8000 cfs in the mid-June heat wave to maintain 68ºF. Late August flows near 7000 cfs were able to bring water temperatures again near 68ºF.

Figure 10. Red Bluff air and water temperatures (average daily) with Wilkins Slough streamflow and water temperatures average daily) in summer of Below Normal water year 2018. There were concerted efforts on the part of Reclamation and its partners to maintain the water temperature standard in summer 2018 after wet year 2017. First, the early summer pulse of 6000 cfs followed by sustained flows near 7000 cfs. The early August 7500 cfs pulse and cooler air brought water temperatures down to 65ºF. Subsequent flow reductions to 6000 cfs were able to maintain the 68ºF standard with the cooler air temperatures.

Figure 11. Red Bluff air and water temperatures (average daily) with Wilkins Slough streamflow and water temperatures (average daily) in summer 2023. Midsummer streamflows <6000 cfs were unable to sustain water temperatures below 70ºF. Cooler air and 5200 cfs briefly brought water temperatures below 70ºF at the beginning of August. Cooler air and sustained flows near 6000 cfs maintained water temperatures below 70ºF in late August.

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.

Sacramento River Spring Pulse Flows – 2024

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The US Bureau of Reclamation (Reclamation), in cooperation with other state and federal agencies, conducted two short-term flow release experiments from Shasta Reservoir in the spring of 2024 to help juvenile salmon reach the ocean. 2024 is a relatively wet year, and it follows a very wet year in 2023 that left a lot of water in storage in Shasta and other Reclamation reservoirs.

The peak emigration to the ocean of wild and hatchery spring-run and fall-run salmon smolts usually occurs in the April-May time period, but may extend into June, especially in wetter years. Reclamation and its partners are developing pulse flow prescriptions for a flow management plan as part of the Action for the Long Term Operation of the Central Valley Project and State Water Project. “Spring pulse flows are designed to improve survival rates of outmigrating spring-run Chinook salmon smolts through the Sacramento River.” 1

The major sources of spring-run salmon smolts include Clear, Battle, Deer, Mill, and Butte creeks, and the Feather River Fish Hatchery. These smolts must pass through the lower Sacramento River, Delta, and Bay. The Feather River Fish Hatchery released its smolts into the lower Feather River in mid-March.

Pulse flows from Shasta Dam pass through Keswick Reservoir, a small regulating reservoir immediately downstream of Shasta Reservoir, and then into the Sacramento River. Pulse flows from Keswick Dam at river mile 300 of the Sacramento River also help move juvenile fall-run salmon downstream. Most Sacramento River fall-run salmon spawn and rear in the 20 miles of the river immediately downstream of Keswick Dam. Pulse flows help move juveniles from this reach downstream to reaches where the flow from tributary rivers and streams augments the flow in the mainstem Sacramento.

The goal of the pulse flows was to release extra flow (3000-6000 cfs) from Shasta reservoir to maintain 11,250 cfs below Keswick Dam for several days (see first pulse in Figure 1). With tributary inflow, river flow near Red Bluff 50 miles downstream was about 15,000 cfs during the first pulse. By the time the first pulse reached Wilkins Slough, nearly 200 miles downstream, the overall flow reached 16,000 cfs (Figure 2), after 3000-5000 cfs of agricultural diversions and multiple tributary inflows. At the end of the pulse flow period, Keswick Dam releases were dropped 6000 cfs (see Figure 1). By May 5, Sacramento River flow at Wilkins Slough had dropped about 8000 cfs. Declining tributary inflows and increased diversions also contributed to the lower Wilkins Slough flows following the pulse flow.

Without adequate flow, juvenile salmon have poor survival during their downstream journey. Low flows increase juvenile salmon’s vulnerability to predation. Low flows also contribute to stressful warm water temperatures. On May 1, 2024, water temperature in the river at Sacramento was below 65oF (18oC), with peak catch of juvenile salmon in the trawl survey (Figure 3). In contrast, in critically dry year 2022, May 1 water temperatures exceeded 65oF, with less than half the 2024 river flow (Figure 4). By late May 2022, water temperatures exceeded 70oF.

In conclusion, the releases of pulse flows from Shasta and Keswick reservoirs had very little signature in the lower Sacramento River due to intervening flows and diversions. The pulse flows were most beneficial in the upper river, where they made up a third to half the river flow. In a wet year like 2024, the benefit is somewhat limited by already high natural flows, although any additional pulse flows later this spring could be of greater benefit with expected declining natural flows and higher air temperatures. In contrast, pulse flows in dry years would provide much greater net potential benefit because of poor natural flows and limited reservoir storage.

The net benefits of pulse flows from Shasta Reservoir must also be considered, of course, in combination with Reclamation’s management of agricultural water deliveries and water stored in Shasta Reservoir for summer temperature management.

Figure 1. Streamflow in the upper Sacramento River below Keswick Dam (RM 300) April 19 through May 19, 2024. Note three-day flow pulses beginning April 23 and May 7.

Figure 2. Streamflow in the middle Sacramento River below Wilkins Slough (RM 120) April 19 through May 19, 2024. Note signatures of the three-day flow pulses show up on April 26 and May 10.

Figure 3. Juvenile salmon trawl catches and water conditions near Sacramento in winter-spring 2024. Note flow pulse in late April.

Figure 4. Juvenile salmon trawl catches and water conditions near Sacramento in winter-spring 2022. There were no flow pulses from Keswick Dam until irrigation releases commenced in May. Catch of juvenile salmon ceased once water temperatures reached or exceeded 70oF in late May.

Klamath River Salmon and Steelhead Recovery – The Future

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After dam removal, the plan for recovering Klamath River salmon and steelhead is relatively straightforward.

Oregon is going to focus on watching to see how steelhead repopulate the upper watershed and on having a more active role in developing spring-run Chinook salmon populations.  Without an existing spring-run stock, Oregon will try establishing one by out-planting stock from California’s Trinity River Hatchery.

California will focus on recovery of existing lower river spring-run Chinook and fall-run Chinook, Coho, and steelhead stocks.  The new Fall Creek Hatchery will sustain the fall-run Chinook, Coho, and steelhead stocks formerly produced at the now-closed Iron Gate Hatchery.  Lower and middle river wild spring–run and fall-run Chinook, Coho, and mainstem and tributary steelhead stocks should expand with improved water quality and access to new habitat.  Historical tributaries offer great potential as does the spring-fed reach of the mainstem near the Oregon border.

In the decades ahead, as the populations and habitat recover, state, federal, tribal, and stakeholder groups will work together toward Klamath salmon and steelhead recovery.

There will be a need to coordinate management of the three H’s:  hatcheries, harvest, and habitat.  Existing hatchery programs should be converted to a single conservation hatchery program focused on salmon and steelhead recovery.  Such a program will need a new hatchery to support the recovery of Klamath spring-run Chinook, as in the San Joaquin River Restoration Program.  The Pacific Fishery Management Council and the two states will have to protect the recovering populations with strict harvest regulations.  Considerable funding will be needed to restore fire-damaged and drought-damaged watersheds, former reservoir footprints, mainstem and tributary fish passage, and spawning and rearing habitat.

Water supply management will remain contested and challenging.  Adequate funding, cooperative efforts, and adaptive management will bring success.

Klamath Dam Removal Update – April 6, 2024

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Video Screen Grab of lower Jenny Creek ASSISTED SEDIMENT EVACUATION PROJECT

In a March 20 post, I related events in the Jan-Feb 2024 period of the Klamath Dam Removal Project.  The initial four-reservoir drawdown in January led to abrupt increases in streamflow, suspended sediment, and low dissolved oxygen levels above and below Iron Gate Reservoir (the lower reservoir).  This was followed by lower stable streamflow, high dissolved oxygen, and declining suspended sediment.  Streamflow pulses from upstream Klamath Lake in late February and early March resulted in (short-term) elevated suspended sediment from exposed sediment erosion in the four reservoir reaches.  These circumstances were expected as part of the four Dam Removal Project.

In March, the Assisted Sediment Evacuation Project began in the Jenny Creek floodplain of the Iron Gate Reservoir footprint.   That project has led to lethal doses of suspended sediment (turbidity) in the lower Klamath River below the Iron Gate Dam site (Figures 1-3).  Project approvals, such as the National Marine Fisheries Service’s (NMFS) biological opinion quoted below, included provisions to stabilize sediments after the January drawdown, but not to flush sediments into creeks and the Klamath River.

Post drawdown and dam removal, crews will be working to actively restore the exposed reservoir footprints and tributary mouths that flow into the former reservoirs. To reduce elevated suspended sediment concentrations (SSCs), the Renewal Corporation will take active measures to flush sediment from the reservoirs during drawdown and then immediately begin stabilizing remaining sediment after drawdown has been completed. Revegetation, channel construction, and placement of habitat features such as logs and boulders will minimize erosion and allow passable channels to form in preparation of fish presence. (NMFS Biological Opinion p. 14)

The origin of the high suspended sediment levels was likely from the exposed bed of Iron Gate Reservoir (particularly the Jenny Creek arm), not upstream reservoir erosion during the Klamath Lake flow pulses.  Sediment levels below Iron Gate Dam were low during the flow pulse that diluted the high sediment loads from Iron Gate Reservoir (Figure 1).  Gages below Copco and JC Boyle reservoirs were lower, generally below lethal levels (Figure 4).

Chinook salmon fry are abundant and most prevalent in the lower Klamath River below Iron Gate Dam in late winter (February-March).  Coho and steelhead fry are more abundant later during spring.

The Assisted Sediment Evacuation Project is slated to end on April 15.  I recommend that it cease immediately, with efforts shifted to “stabilizing remaining sediment,” in order to minimize impacts of the project on Klamath River salmon and steelhead.

Figure 1. Turbidity and streamflow in the Klamath River below Iron Gate Dam (rm 193) in January to March 2024. Note turbidity of 300-500 SBU is roughly 1000-2000 mg/l total suspended sediment (TSS). Such levels are considered lethal for juvenile salmon and steelhead.

Figure 2. Turbidity and streamflow in the Klamath River near Seiad Valley below the mouth of the Scott River (rm 145) in March 2024.

Figure 3. Turbidity and streamflow in the Klamath River near Seiad Valley about ten miles upstream from the mouth of the Scott River (rm 145) in March 2024.

Figure 4. Turbidity and streamflow in the Klamath River just upstream of Iron Gate Reservoir and below Copco dams in March 2024.