Category Archives: Bay-Delta

Increasing River, Delta, and Bay Summer Freshwater Flows Proves Viable Action

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In Above Normal water year 2024, an increase in summer freshwater flows released from reservoirs to the Bay-Delta estuary has proven a viable action to reduce threats to Central Valley fishes.  Water management actions in early July heat waves alleviated extreme water temperatures that threaten the native fishes in rivers and the Bay-Delta.  These actions can be described as adaptive management experiments to test their potential performance for the update of the State Board’s Bay-Delta Plan. 

Actions

  • Increasing lower Sacramento River flow from 5000 cfs to near 8000 cfs has helped lower Wilkins Slough gage (WLK) water temperatures from 70-72oF to the water quality standard of 68oF (Figure 1), despite record-high air temperatures (Figure 2).
  • Increasing Delta inflow at Freeport (FPT) from 14,000 cfs to 20,000-22,000 cfs (a combination of increased Wilkins Slough, Feather River, and American River flows) has lowered Freeport water temperatures in the north Delta from 72oF to 70oF (Figure 1).
  • A rise in Delta outflow from 8,000 cfs to 12,000 cfs has helped reduce Rio Vista (RVB) water temperatures at the Delta’s exit to the Bay from 75-76oF during the early July heat wave to 72oF after the heat wave (Figure 2).

Benefits

The actions may not seem that dramatic, but they are very important to the river, Delta, and Bay environments and to the salmon, smelt, steelhead, sturgeon, and other native Central Valley fishes that depend on these habitats.  Water temperatures in the 72-75oF range are highly stressful or lethal to these native fishes.  Such temperatures favor non-native predatory and competing fishes.  Water temperatures of 68-72oF are at the upper favorable limits for the native fish and are necessary to maintain viable growth, survival, and reproduction.  These temperatures also help ensure that dissolved oxygen is adequate and that algae blooms do not reach excessive levels.  In other words, they promote a healthier ecosystem.  Water temperatures near or above 75oF, which occurred in the Delta of drought years 2021 and 2022 (Figure 3) under extreme low flows (Figure 4), are deadly to native Delta fishes.

Conclusion

Although water managers in 2024 probably did not have these bold actions in mind to save fish (flows were increased to allow maximum summer water diversions from the Delta), their fortuitous implementation clearly highlights early summer flow measures that should be included in the update of the Bay-Delta Plan.  Two additional actions I would recommend are higher flows in the San Joaquin River to provide some minimal benefit to the San Joaquin’s native fish community, and reductions in water exports.

Figure 1.   DTO = Delta Outflow to the Bay, FPT = Sacramento River Freeport gage, WLK = gage below Wilkins Slough on lower Sacramento River upstream of the Delta, RVB = Rio Vista Bridge in Sacramento River channel northwest Delta, near entrance to eastern Bay.

Figure 2.  Average daily air temperatures at Red Bluff (KRDD) in Sacramento Valley, Modesto (KMOD) in San Joaquin Valley, and Rio Vista Bridge (RVB) in west Delta May-July 2024.  Note Delta air temperatures are generally 5-15oF lower in the Delta than the valleys.  Also note the record or near-record air temperatures in early July.

Figure 3.  Average daily water temperatures in the north Delta channel of the Sacramento River at Freeport May-July 2021-2024 and average of years for decade 2001-2010.

Figure 4.  Average daily (tidally filtered) streamflow in the north Delta channel of the Sacramento River at Freeport, May-July 2021-2024 and average of years for decade 2001-2010.

Bay Warms in July 2024

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This is a follow-up to a July 8 post on summer 2024 aquatic habitat conditions in the Bay-Delta Estuary.  In this post, I focus on mid-July conditions after yet another summer heat wave.  I am concerned that conditions are building for yet another sturgeon die-off this summer.  Sturgeon mortality is caused by excessively warm water and algae blooms that eventually lead to rapid algae die-off and associated extremely low dissolved oxygen levels (<5 mg/l) throughout the Bay.  Such conditions became acute in summer of drought year 2022 and led to the deaths of thousands of adult sturgeon and other Bay fishes. 

Conditions in the Bay are already worse this year at the beginning of summer than in 2022 or 2023 (Figure 1).  Water temperatures and chlorophyll concentrations are higher, with dissolved oxygen concentrations falling.

Figure 1.  Water temperature (C), dissolved oxygen (mg/l), and chlorophyll concentration (micrograms per liter) in Grizzly Bay 2022-2024.

Of greatest concern is the already warm water temperatures in parts of the Bay-Delta despite a relatively high Delta inflow with cooler than normal water temperatures (Figure 2).  Water temperatures have exceeded 75oF in the west Delta and east Bay low-salinity zone of the estuary (the prime summer habitat of endangered Delta smelt).  Water temperatures of 75-77oF (24-25oC) are lethal to Delta smelt.1

In the decades of the 80’s and 90’s, Delta smelt were still relatively abundant although suffering severely in drought years.  Water temperatures rarely exceeded 70oF in Suisun Bay (Figure 3).  The reason for the difference is likely a combination of higher air temperatures, lower Delta outflows, and higher Delta water diversions in recent decades.  In some years lower, warmer Delta inflows aggravate the problem, but not this year (2024) when inflows were kept high to sustain high Delta water diversions.

One area of warming of the lower Sacramento River channel that deserves special attention is the north Delta below the Delta Cross Channel and Georgianna Slough bifurcation.  Much of the water destined for south Delta exports is diverted from the Sacramento River through these channels.  In the reach below the diversion channels the river temperature increased several degrees (73 to 76oF) in early July.  One explanation is that of the 21,000 cfs Delta inflow at Freeport only 5000 cfs remained below the entrance to Georgianna Slough (Figure 4).  The missing flow passed into Georgianna Slough, the Delta Cross Channel, and Miners/Steamboat Sloughs, all reaches where the flow warmed to even a greater degree.  At Rio Vista and the west Delta, where the water exits the Delta for the Bay, water temperatures reached 76oF as total outflow increased to 10,000 cfs from the 5000 cfs in the lower Sacramento River channel and 5000 cfs returning warmer water from the Cache Slough complex and San Joaquin River channel.  Waters in the wide, large, open channel at Rio Vista also slowed, with a stronger influence of the tides, especially during the recent heat waves (Figure 5). 

I contend that the high rate of Delta water diversion at Georgianna Slough and the Delta Cross Channel contributed to the warming by forcing cooler water from the Sacramento River Delta inflow into the central Delta where it warmed or was diverted.

I recommend closing the DCC and reducing Delta water diversions in July and August to reduce Bay-Delta water temperatures and minimize the potential for excessive algae blooms, low dissolved oxygen, and sturgeon die-offs in the Bay this summer.  I further recommend that Delta inflows be sufficient to maintain water quality standards for water temperatures in the lower Sacramento River above the Delta.

Figure 2. Bay-Delta conditions showing daily average flows in blue and purple, maximum daily water temperatures in red on or about July 12, 2024.
Figure 3.  From Baxter et al 1999 Figure 7.
Figure 4.  Sacramento River flow and water temperature downstream of the entrance to Georgianna Slough, April-July 2024. Note the effect of two closures of DCC in early June that forced more water down the Sacramento River channel cooling the river below slightly.  Opening of the DCC at the beginning of June reduced flow and increased water temperature in the river below Georgianna Slough.  Note also that at the lower net flows, the effect of the tides was greater, slowing transit net flow rate, which likely increased the rate of warming.
Figure 5.  Air and water temperature at Rio Vista Bridge June 1 to July 1, 2024. Note the 1 to 2.5oF influence of heat waves on water temperature.  The heat wave at the beginning of July with an average daily temperature of 90oF is exceptional for Rio Vista.

  1. It is unlikely Delta smelt would survive extended periods above 72oF; they would not do well in water temperatures above 68oF. ↩

Exports and Bay Delta Habitat – Early July 2024

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This is an update on my last several posts on spring habitat conditions in the Bay-Delta in this Above Normal water year.  After a wet winter-spring with good Delta and Bay conditions in Above Normal water year 2024, June 2024 water project operations returned the river, Delta, and Bay to drought-year conditions.  I warned in late June that habitat conditions (flows and water temperatures) were getting bad and that a forecasted heat wave could make conditions even worse.  It’s happened.

The State Water Project (SWP) and the Central Valley Project (CVP) started moving water south in earnest at the beginning of July.  Shasta, Oroville, and Folsom reservoir releases increased, raising Delta inflow at Freeport to 20,000 cfs (Figure 1).  SWP south Delta exports are at maximum at 6,000 cfs (Figure 2).  CVP south Delta exports were already maxed out at 4,000 cfs.  The Sacramento River contractors also removed their portion of the Shasta pie (6,000 cfs, Figure 3), to make the total water project haul from the Sacramento Valley 16,000+ cfs.  Note this total does not include water diverted upstream of the Delta from Sacramento tributaries or from the San Joaquin River and its tributaries.

Impact to Freeport Water Temperature

On the positive side, the increased Delta inflow at Freeport dropped water temperatures slightly at Freeport as the heat wave commenced (Figure 4).  I contend that the water temperature would have increased significantly with heat wave if the flow had not increased.

Impact to Rio Vista Water Temperature

On the negative side, the main problem from the state action was increased water temperature at Rio Vista (to 75oF) due to the combination of higher south Delta exports, high air temperatures, and lower Delta outflow (Figure 5).  I contend that slightly higher Delta inflows and lower south Delta exports (thus, higher Delta outflow and higher net Rio Vista flows) could have kept Rio Vista water temperatures closer to 72oF.

Impact to Lower Sacramento River Water Temperature

On the positive side, the increased flow in the lower Sacramento River from the Shasta Reservoir releases (see Figure 1) kept lower Sacramento River water temperatures from increasing during the heat wave (Figure 6).  That experiment proved the potential benefit of such an action on its own

Impact to Bay Water Temperature

Bay water temperature during the early July heat wave also increased to 74-75oF during ebb tides, as warm Delta (Rio Vista) water entered the eastern Bay (Figures 7 and 8).  On flood tides, cooler 68-70oF water returned to the eastern Bay.  After several days of these conditions, the eastern Bay warmed by 2-3oF.  I contend that if Delta outflow had not dropped to 8000 cfs with the higher south Delta exports, and the Delta (Rio Vista) had thus been maintained closer to 72oF, that Bay temperatures would have been several degrees cooler (likely less than 72oF).

Conclusion

The State Water Project should not have started full transfer of Sacramento Valley reservoir water to southern California via its south Delta export pumps during an early July heat wave.  Such action compromised San Francisco Bay’s already-stressed environmental conditions, which could lead to fish die-offs in the Bay again this summer.

Figure 1.  American (AFO), Feather (GRL), and Sacramento River (WLK) flows, making up Delta inflows at Freeport (FPT) May 15-July 5, 2024.

Figure 2.  Delta outflow (DTO) and CVP’s Tracy (TRP) and SWP’s Harvey Banks (HRO) export rates 6/1-7/5, 2024.

Figure 3.  Sacramento River June 2024 streamflows at Keswick Dam (RM 300) and Wilkins Sough (RM 120) gages.  Diversion loss equals difference plus above-Wilkins tributary inputs.


Figure 4.  Sacramento River channel flow and water temperature at Freeport (FPT), 5/1-7/5 2024.

Figure 5.  Water and air temperature at Rio Vista Bridge gage with Delta Outflow 5/15-7/5, 2024.


Figure 6. Sacramento River channel flow and water temperature at Wilkins Slough (WLK), 5/1-7/5 2024.

Figure 7.  Tidally filtered salinity and water temperature in eastern Suisun Bay near Pittsburg, CA. 6/15-7/5, 2024.

Figure 8.  Salinity (EC) and water temperature in western Suisun Bay at Benicia Bridge near Benicia, CA. 6/28-7/5, 2024.

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.