Butte Creek Salmon – 2022 Update Guest Post by Allen Harthorn, Executive Director, Friends of Butte Creek

The 2018 run of spawning adult spring-run Chinook salmon in Butte Creek was not abundant by Butte Creek standards.  These were the offspring of the 2015 drought-year run.  California Department of Fish and Wildlife (CDFW) estimated only around 2000 spawning adults in 2018, in the lower 25% percentile of the population counts since 1995. The first egg laying in 2018 happened in late September, and the last of the spawners finished their dance around the middle of October. Carcasses were counted, the wildlife of the creek had been feasting for weeks.

The wait began for the eggs in the gravel to “eye up,” a point where the eggs are known to have been successfully fertilized. Several weeks later, depending on water temperature, the alevin juveniles “button up”, or finish feeding off their yolk sack and started feeding on their own as fry. Fry juveniles were captured by CDFW in November, some early in November. This is fairly rapid salmon development for spring-run salmon, but Butte Creek, where the fish spawn, is one of the warmest stream reaches supporting spring-run Chinook.

Early on November 8th of 2018, a black cloud rose rapidly over Butte Creek. The Camp Fire began at 6:30 in the morning. It raced across two ridges and the 3-mile-wide West Branch Feather River canyon, and exploded across Paradise and Magalia and down Little Butte Creek Canyon like a torch. Another section burst off the ridge above Centerville and Helltown. By the next morning, 80% of the canyon downstream of Helltown had burned. Hundreds of homes were leveled. The fire meandered through the canyon for two weeks.

As storms began to approach California, a massive effort to try and control the potentially toxic runoff and pollution was initiated by Friends of Butte Creek and the US Fish and Wildlife Service. They placed many miles of straw erosion control wattles around most all of the burned-out structures. When the heavy rains began, it seemed like there was nothing more that could be done to save the emerging salmon. The creek ran black with ash, soil, and debris. Monitoring on Little Butte Creek, which drains much of Paradise, showed high levels of many toxic chemicals, including arsenic. Although the salmon seemed insignificant in light of the destruction from the fire, biologists were worried that there would little success from this small 2018 run.

Early in March of 2021, an amazing sight began surging through the Butte Creek system. Despite a seriously dry winter and relatively low flow in the creek, salmon started showing up in great numbers. Schools of 10-50 fish were sighted throughout the system. By late March, many thousands of spring-run salmon were making their way into the middle canyon reach below Centerville where cool, deep pools provide the most important refuge for these fish to make it through the summer. In April, at one of the monitoring pools with the easiest access, nearly 800 fish held in one pool.

Downstream, water diversion dams in the valley sections of Butte Creek were in pretty good shape after many years of upgrades to the ladders and screens, allowing salmon to reach the upstream holding pools earlier and in better condition than years past. Late arrivals in the past often showed damage to their skin from concrete dams and ladders, and had low spawning success rates.  Fungus often covered the eyes of these late-arriving fish, and many did not make it through the summer.

Figure 1. Weir 1, May 2012. CDFW Photo.

Figure 1. Weir 1, May 2012. CDFW Photo.

In April 2021, a number of early-arriving fish uncharacteristically showed up with serious damage to their heads. Not much later, word began to spread that water had been shut off at one of the weirs in the Sutter Bypass, and many spring-run salmon had perished. Apparently, some salmon that did make it past the dam suffered injuries in the process. Additionally, the low flow in the Sutter Bypass may have led hundreds of Butte Creek salmon to continue on up the Sacramento River to Colusa where Butte Creek originally entered the river at the Butte Slough Outfall gates. The gates were closed, but the fish sensed this was a potential access to Butte Creek and began bashing their heads and bodies on the outfall gates. It took many days for the Department of Water Resources to open the gates for fish, and many damaged salmon surged into the creek. At times in late April and early May, as many as 10% of the fish showed signs of damage.

Most significant was the size of the run that looked to be the biggest run of spring-run Chinook salmon to ever return to Butte Creek, all from the parent spawning population of about 2000 fish.

California Department of Fish and Wildlife biologists began doing snorkel surveys in June and quickly began estimating over 10,000 adult returnees. Local observers, including this author, estimated over 20,000, rivaling the 20,000 estimated returnees of 1998. The sight was spectacular, and optimism was high that something about the Camp Fire may have contributed to the success of the juveniles from that fateful fall in 2018, along with the wet winter in 2019.  Successful salmon populations may benefit from nutrient releases, sediment and ash cover for their downstream migration, or for other unknown elements of the cycle.  The extra nutrients, and the high flows and water levels in the Butte Basin and Sutter Bypass in winter 2019, were likely beneficial.

The downside of this huge run of fish became apparent in summer 2021. High air temperatures in mid-June pushed the thermometer over 100 degrees F. for several days, and water temperatures in Butte Creek soared. Meanwhile, operations of the imported West Branch Feather River water for PG&E’s DeSabla powerhouse hit a snag when one shallow (and warm) West Branch reservoir (Round Valley Reservoir) ran out of water earlier than expected. This led to a drop in flow that affected Butte Creek for about 24 hours (Figure 2 below). Colder water was released from another West Branch reservoir (Philbrook) a day later and quickly moderated temperature in the creek, but the brief drop in flow came about the same time as the start of the disease outbreak among the holding salmon in Butte Creek. Water temperatures began to rise above 19.8 degrees Celsius soon after the flow drop on June 23 (Figure 3 below). Dead fish afflicted with Ich and Columnaris began turning up in the pre-spawn mortality survey just a week later. Another two weeks later, hundreds of dead fish began rotting in Butte Creek or were dragged off by opportunistic wildlife. By the end of July, when surveys were interrupted by smoky conditions from the Dixie Fire, almost 14,000 pre-spawn mortalities had been counted.

Figure 2. Water import from West Branch Feather River to Butte Creek, June 22-27, 2021.
Source: California Data Exchange Center

Figure 3: Recorded mean water temperature (ºC) within the 3 holding pool locations along with numbers of pre-spawn moralities recorded throughout the pre-spawn mortality survey.
Source: CDFW Butte Creek Spring-Run Chinook Salmon Adult Monitoring Report 2021

Butte Creek is the most productive salmon stream in California and is the home of what is far and away the state’s most important spring-run Chinook population. However, following a year with good production, good juvenile rearing conditions, good ocean conditions, but nearly 92% pre-spawn mortality, one has to wonder if the management and operations of Butte Creek in Butte Creek Canyon under the current configuration of infrastructure are ever going to be able to provide reliable conditions for spring-run salmon to thrive. Although 2021 was the hottest summer on record in California, new records seem to be set almost every year. The Quartz Bowl (Figure 4 below), where most of the 1807 spring-run that survived in 2021 managed to stay alive, is no longer the refuge it has been in the past.

Figure 4. Quartz Bowl Pool, August 2021. Photo by John Sherman.

The salmon spawning reaches of Butte Creek, upstream of the old Covered Bridge near the intersection of Honey Run Road and Centerville Road in Butte Creek Canyon, are largely managed under PG&E’s DeSabla-Centerville Hydroelectric Project, FERC Project No. 803. The Project notably features diversion of water from Butte Creek into the Butte Canal and diversion of water from the West Branch Feather River into the Hendricks Canal and the Toadtown Canal. At the bottom of these canals is DeSabla Forebay (Figure 6 below), a ~200- acre-foot reservoir located next to Skyway (road) on the ridge uphill from the town of Paradise. Water collected in DeSabla Forebay is dropped through a “penstock” (pressurized pipe) into DeSabla Powerhouse, from which it is discharged into Butte Creek. DeSabla Powerhouse is located right next to Butte Creek, about two miles upstream of the Quartz Bowl Pool, the current upstream limit for Butte Creek’s spring-run salmon.

The DeSabla-Centerville Hydroelectric Project’s import of water from the West Branch Feather River helps provide additional cool water for spring-run salmon holding in Butte Creek when managed properly. Maintaining this import of water in some form is essential to the long-term viability of spring-run salmon in Butte Creek.

Historically, PG&E also diverted water at Centerville Head Dam, less than a mile downstream of DeSabla Powerhouse, into Lower Centerville Canal, where water flowed about 6 miles downstream to pass through Centerville Powerhouse, whose outfall re-entered Butte Creek near the community of Centerville. Centerville Powerhouse has been inoperable since 2011, and PG&E has not diverted water into Lower Centerville Canal since 2013.

Figure 5. Map of the DeSabla-Centerville Project and area, from February 2017 PG&E flyer distributed simultaneous to PG&E’s request to FERC to withdraw its application for a new project license.

In October 2004, PG&E began the process of seeking a new hydropower license from the Federal Energy Regulatory Commission (FERC) for the DeSabla-Centerville Project. The relicensing was largely complete with the State Water Board’s issuance of a final water quality certification for the relicensing, revised  in 2016. A biological opinion from the National Marine Fisheries Service (NMFS) for protection of Butte Creek’s spring-run salmon and steelhead under the Endangered Species Act was the last major remaining step before FERC’s issuance of a new hydropower license.

However, in February 2017, PG&E withdrew its application for a new license, announcing its intention to sell the project. FERC disallowed the withdrawal, but held the licensing process in abeyance pending potential sale.

Five and a half years later, on August 16, 2022, PG&E informed FERC that negotiations to sell the project had ended without sale, and PG&E requested that FERC complete the relicensing process. In the interim, none of the conditions that FERC and the State Water Board were poised to require of PG&E in the new project license have been implemented. Most notable among measures not yet implemented is a device to reduce heating of water as it is held in and passes through DeSabla Forebay. NMFS called out the need for such an infrastructure improvement in a Preliminary Biological Opinion in 2006.

Figure 6. DeSabla Forebay and intake tower to DeSabla Powerhouse. The reservoir is almost totally unshaded; ambient summer temperatures are frequently in the 90’s and above. Photo by C. Shutes.

The mass pre-spawn mortality in 2021 put an enormous exclamation point on the urgency of completing upgrades in the DeSabla hydroelectric project. It should also cause fisheries managers and advocates to revisit decisions about whether a large-scale reconfiguration of infrastructure is needed to keep water imported from the West Branch cold enough to benefit spring-run salmon in Butte Creek. Admittedly expensive options like piping all or part of the Hendricks and Toadtown canals, or bypassing them with a tunnel, may be required. Outside funding may also be required.

Perhaps the best and most durable solution, and one that is being tested elsewhere, is to get the fish upstream to colder water. Three separate studies completed in 1997, 1998, and 2000 by Holtgrieve (CSU Chico), Kier Institute for Fisheries Resources, and Watanabe (CDFG) indicated that there is good habitat upstream, and all recommended further study.

There are problems with fish passage to the upper reaches of Butte Creek. These include natural barriers, such as that at Quartz Bowl, about which fisheries managers have traditionally been squeamish (a notable exception is a recently completed fish ladder past a natural barrier on Deer Creek), and also the no-longer-used Centerville Head Dam (Figure 7 below), which has no fish ladder.

There are also problems with diversion of water out of Butte Creek by the DeSabla Project (into the Butte Canal) and by the nearby Forks of Butte Project, the latter recently offered for sale.

In the past, fisheries managers concluded that the difficulties and costs of fish passage and major new infrastructure outweighed the potential benefits. But given the reality of climate change, increasing temperatures, and greater frequency of drier dry years, it is high time to revisit the tradeoffs. Large-scale improvements may provide value that is well worth the costs to save the extraordinary run of spring-run salmon in Butte Creek.

Figure 7. Centerville Head Dam. Photo by Allen Harthorn.

Figure 8: Butte Creek annual escapement and pre-spawn mortalities, 1956-2021. Figure created by Friends of Butte Creek.

 

Allen Harthorn

Executive Director

Friends of Butte Creek

Cache Slough Tidal Wetland Restoration – Update More misguided resource-damaging habitat restoration for an already highly altered and compromised Delta

Cache Slough Complex Restoration

The Cache Slough Complex is in the lower (southern) Yolo Bypass in the north Delta region (Figure 1). It is the focus of the state’s tidal wetland restoration EcoRestore Program that spans 16,000 acres in the Cache Slough region of the Sacramento-San Joaquin Delta.

The 53,000-acre Cache Slough Complex is located in the northwest corner of the Sacramento-San Joaquin River Delta in Solano and Yolo counties (Figure 1). The Yolo Bypass receives inflow directly from the Sacramento River (Fremont Weir), the Colusa Basin Drain, Putah and Cache creeks, and agricultural and municipal discharges. The Cache Slough Complex exits the Yolo Bypass via Cache Slough, first connecting to the outlets of Miner and Steamboat Sloughs, before entering the tidal Sacramento River channel near Rio Vista.

The Cache Slough Complex has been identified as an area with great potential for tidal restoration as a result of its connectivity with the Yolo Bypass floodplain, suitable elevations, high turbidity, high primary and secondary productivity, and use by Delta smelt (Hypomesus transpacificus), Chinook salmon (Oncorhynchus tshawytscha), and other native fishes. Both federal and state wildlife agencies consider the Cache Slough Complex to be a prime area to advance habitat conservation to benefit endangered species in the Sacramento-San Joaquin Delta and incorporate improvements to the regional flood management system.

The latest project approved for construction is the Lookout Slough Project, a 3000-acre tidal marsh restoration immediately to the west of Liberty Island. The Project was certified by DWR in 2020 as mitigation/compensation for the Delta Tunnel Project. The Delta Stewardship Council recently denied appeals1 to the state’s certification of the Lookout Slough tidal marsh restoration project. Once completed, Lookout Slough will be the Delta’s largest single tidal habitat restoration project to date.

The Problem

Most of the tidal “restoration projects” in the Cache Slough Complex involve breeching leveed tracts of agricultural land to create subtidal or intertidal habitat. Tidal waters once confined to narrow floodplain channel are now allowed to pour through breaches onto over 10,000 acres of formerly diked farmlands. The process started between 1980 and 2000 when Little Holland Tract (1456 acres) and Liberty Island (4340 acres) levees failed and were not repaired, leaving these lands open to the tides. Because these reclaimed wetlands had subsided during active farming, most of the “restored tidelands” became sub-tidal, year-round, warm, shallow, open-water habitat. Such habitat is too warm for Delta native fishes except during the winter.

The enhanced tidal exchange and warm productive winter and early-spring habitat attracts migratory Delta native fishes like smelt, splittail, and salmon to the Cache Slough Complex. While such habitat is considered beneficial in winter, it warms excessively in spring and summer, reducing the period of quality rearing, and can reduce overall survival and production. Native fishes have succumbed to the heat, stranding in the uneven landforms, and predation by non-native warm-water fish.

The latest projects, Lower Yolo Ranch (1749 acres), Yolo Flyway Farms (300 acres), and Lookout Slough (3000 acres), will add 5000 acres of mostly shallow intertidal habitat. Tidewater will flood onto these lands twice a day to warm in the California sun and then return to cooler deep, shaded, sub-tidal sloughs long considered prime Delta smelt and salmon rearing habitat. Not only will the new inter-tidal “wetlands” be too warm, but they will contribute to warming adjacent sub-tidal sloughs that convey water to and from other parts of the north Delta. This water quality degradation gets worse with each new project and has resulted in the degradation of the entire north Delta as a viable spawning, rearing, and critical habitat of Delta smelt. The effect has measurably contributed to the near extinction of Delta smelt.

The Evidence

The United States Geological Service has many water quality and flow monitoring gages in the Cache Slough Complex (Figure 2) that provide considerable evidence of the above-described problem. Specific gages with pertinent data records reviewed for this post are highlighted in Figure 2.

Waters in the northern Cache Slough Complex become too warm for salmon and smelt (>20ºC) by spring (Figure 3). In summer (Figure 4), water tidally flooded into subtidal island-tracts can warm 5-7ºC over a day before draining back into adjacent sloughs. Water temperatures in the northern sloughs of the Cache Slough Complex reach 25ºC (lethal to smelt) or higher in summer, even in wet and normal water years (2016-2018, Figure 5). Water temperatures in the southern Cache Slough Complex are only slightly lower (Figure 6). Over the past decade, water temperatures in the Cache Slough Complex overall have been gradually increasing (Figures 7 and 8), to the detriment of Delta native fishes.

The Solution

The problem can be lessened or even reversed at existing and future restoration projects by:

  1. Limiting tidal access to sub-tidal sites to winter, when water and air temperatures are colder.
  2. Building projects with flow-through tidal channel features rather than a single opening.
  3. Ensuring that projects are inter-tidal with small, narrow, shaded channels, or tule benches.
  4. Narrowing, deepening, and shading connecting tidal sloughs.
  5. Limiting discharge of warm agricultural wastewater into tidal channels.
  6. Providing supplementary inflow of Sacramento River water from the Fremont Weir, from the entrance gates of the Sacramento Deepwater Shipping Channel, or from other locations.
  7. Retrofitting existing restoration sites and designing future projects as outlined above.

 

Figure 2. USGS gage locations in the Cache Slough Complex.

Figure 3. Water temperatures recorded at Little Holland Tract in 2015-16.

Figure 4. Water temperatures and water surface elevation (gage height) recorded at Little Holland Tract in July 2017. Note higher water temperature spikes occurred with strongest ebb (draining) tides.

Figure 5. Water temperature in Liberty Cut adjacent to Little Holland Tract, 2016-18.

Figure 6. Water temperature and tidally-filtered flow rate in Sacramento Deepwater Ship Channel, April-September 2021.

Figure 7. Water temperature in lower Cache Slough, 2011-2016.

Figure 8. Water temperature in the lower Sacramento River channel near Rio Vista, 2010-2019.

Over-Summering Spring-Run Chinook Salmon in Mill Creek and Deer Creek

In a recent research paper, authors Cordoleani, Phillis, and Sturrock describe what they call a “rare” life history of spring-run Chinook salmon in Mill Creek and Deer Creek, tributaries to the Sacramento River. The authors suggest that this life history is becoming increasingly important in our warming climate.1 For more discussion of this topic, see alsohttps://fishbio.com/worth-waiting-for-the-advantages-of-late-migrating-spring-run-chinook/. The authors’ abstract for the paper provides the following summary:

ABSTRACT: Rare phenotypes and behaviours within a population are often overlooked, yet they may serve a heightened role for species imperilled by rapid warming. In threatened spring-run Chinook salmon spawning at the southern edge of the species range, we show late-migrating juveniles are critical to cohort success in years characterized by droughts and ocean heatwaves. Late migrants rely on cool river temperatures over summer, increasingly rare due to the combined effects of warming and impassable dams. Despite the dominance of late migrants, other strategies played an important role in many years. Our results suggest that further loss of phenotypic diversity will have critical impacts on population persistence in a warming climate. Predicted thermally suitable river conditions for late migrants will shrink rapidly in the future and will be largely relegated above impassable dams. Reconnecting diverse habitat mosaics to support phenotypic diversity will be integral to the long-term persistence of this species.

What the authors of this study are noting is the two dominant life history patterns of Chinook salmon: subyearling and yearling smolt production, or “ocean” type vs. “river” type Chinook. One type or the other often dominates in a particular river system, but often both types exist, providing for a diversity of life history that protects the species from extinction.

The main difference is that the subyearling or ocean type leaves for the ocean, estuaries, and coastal waters in late winter or spring, whereas the river type over-summers in rivers before emigrating to the ocean in the following fall or winter.

Technically speaking, neither “type,” “behavior,” or “strategy” is “rare” (or “overlooked”). The ocean type occurs in many river systems, especially in the Chinook salmon’s southern range, which provides conditions for rapid winter growth that allows young salmon to reach smolt size by spring – “early” outmigrants. Slow growth, more common in the colder northern range of Chinook, often requires young salmon to “over-summer” in rivers to reach smolt size to migrate to the ocean.

Spring-run Chinook have adapted to colder, higher elevation streams, especially in their southern range in California’s Central Valley. In contrast, fall-run Chinook spawn in lower elevation streams or lower portions of coastal, Central Valley, and Klamath-Trinity rivers. The spring-run tend to be more river type because of the colder water and longer journeys, whereas fall-run are faced with warmer water and shorter journeys. Fall-run also tend to rear in estuaries.

In Central Valley rivers, most of the historical populations of spring-run Chinook have been cut off from the higher elevation spawning reaches. They are forced to spawn below rim dams, and populations specific to many rivers (such as the American) have not survived. For populations that survive downstream of rim dams, the ocean type strategy pre-dominates, though in the coldest tailwaters of rim dams, some over-summering is possible, and the river type life history occurs for both spring-run and fall-run Chinook. In drought years, tailwaters may become too warm, and river type smolt production suffers.

In Central Valley rivers where no major dams occur, such as Mill Creek and Deer Creek, both life history strategies occur. The authors document that more than half of the adult spring-run sampled over a 12-year period that returned to Mill and Deer creeks had emigrated from their natal streams using a river type life history. The trend was more pronounced for drought years.

The authors emphasize the importance of cold-water habitats in higher-elevation rivers and the river type life history for spring-run Chinook as the climate warms. Yet there are additional factors that should be considered in evaluating why the spring-run populations in Mill and Deer Creek are so heavily dependent on the river type life history. These other factors are related to lack of rearing habitat in the lower reaches of these streams and to the dependence of their outmigrating juvenile salmon on flows, including in the Sacramento River.

A look at the CDFW Grand Tab for escapement of Central Valley spring-run Chinook (pp. 8-9) shows Mill Creek and Deer Creek haven’t reached 1000 adult fish returning to either stream since 2006. In contrast, returns to Butte Creek are perennially in the thousands. and in four years since 2006 topped 10,000. In large part, this is because there is abundant rearing habitat in the Butte Sink and Sutter Bypass complex for Butte Creek spring-run juveniles. Mill Creek and Deer Creek don’t have substantial low-elevation rearing habitat accessible to juvenile spring-run.

So while the river type life history appears to be a viable strategy to help save the spring-run populations in Mill Creek and Deer Creek from extinction, it has not yet shown itself to be a viable strategy for recovery comparable to the elements present on Butte Creek.

Reports by the California Department of Fish and Wildlife (formerly Fish and Game ) document the relative success of the river type life history for spring-run juveniles in Butte Creek.2 However, successful returns of river type spring-run in Butte Creek (measured in single digits) are grossly overshadowed by overall escapement.

A major common trait of spring-run Chinook that survive to escapement, both among river type spring-run in Mill Creek and Deer Creek, and among ocean type and river type spring-run in Butte Creek, is that they are well positioned to emigrate to the Delta and Bay as large smolts in the December-March time period. This is the most likely time for flows in the Sacramento River that have sufficient magnitude to allow successful downstream migration and rearing in the Sacramento and the Delta. It is also necessary in all three of these tributaries to the Sacramento, because agricultural diversions ramp up substantially in mid-April, and flows on the valley floor in these streams then become much more difficult to navigate than before April.

In summary, the authors’ characterization of the “river” strategy as “rare,” especially for spring-run Chinook, is not accurate. Nonetheless, the difficulty of maintaining the river type life history strategy because of drought and global warming for Central Valley spring-run and fall-run Chinook is increasing on the valley floor. Furthermore, the “ocean” strategy for both spring-run and fall-run Chinook suffers the most from drought and global warming as the rearing and emigration windows of the lower rivers and estuary shrink.

Improved access to thermally suitable higher elevation streams, including habitat upstream of rim dams, is going to be essential under a warming climate in the future. A river type life history may play an increasing part. However, the contrasts in escapement of spring-run Chinook between Mill and Deer Creeks on the one hand, and Butte Creek on the other, show the importance of also establishing and maintaining connectivity to quality rearing habitats on or near the valley floor. Migration habitat, or sufficient flows in the lower reaches of the Sacramento River and its tributaries, is a third key element of recovering spring-run and other runs of Central Valley Chinook salmon.

  1. Cordoleani, F., Phillis, C.C., Sturrock, A.M. et al.Threatened salmon rely on a rare life history strategy in a warming landscape.  Clim. Chang.11, 982–988 (2021). https://doi.org/10.1038/s41558-021-01186-4.
  2. See, e.g., Ward, P.D., McReynolds T.R., and Garman, C.E., Spring-Run Chinook Salmon, Oncorhynchus Tshawytscha, Life History Investigation 2002-2003, 2004, DFW Ref # 90573, p. 2: “The limited sample suggests that However, the yearling Butte Creek spring-run survive at a rate significantly higher than YOY emigrants.”  Available at: https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjNmuCEh_b3AhX0KkQIHYIDA6cQFnoECAYQAQ&url=https%3A%2F%2Fnrm.dfg.ca.gov%2FFileHandler.ashx%3FDocumentID%3D32894&usg=AOvVaw28r2uoKbLqAvzrCljBoX7ASee also McReynolds, et al CDFW, Butte and Big Chico Creeks, Spring-Run Chinook Salmon, Oncoryhnchus Tshawytscha, Life History Investigation 2004-2005, 2006, Ref # 90754, Table 1 p. 9. Shows yearling outmigrants trapped in 2004. See also Appendix B, figure 1.  Available at: https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&ved=2ahUKEwic4J20mvf3AhVZoY4IHaqGCu8QFnoECAQQAQ&url=https%3A%2F%2Fnrm.dfg.ca.gov%2FFileHandler.ashx%3FDocumentID%3D32895&usg=AOvVaw2Z7RFTthJ03e6d0IkW0by2.

State and Federal Hatcheries Release Salmon Smolts to Rivers, Delta, Bay, and Coast

Hatcheries in California are releasing tens of millions of salmon smolts in 2022, per normal operations.  State hatcheries are trucking over ten million fall-run salmon to the Bay again this spring because of the drought.  State and federal hatcheries are releasing another ten million-plus fall-run smolts to the rivers near the hatcheries.

Future salmon fisheries will depend mostly on the Bay releases, because few of the hatchery smolts released to the river or wild salmon smolts will survive the journey to the ocean this drought year.  Yet even the prognosis for smolts released to the Bay is poor.  Delta outflows near 4000 cfs under the State’s TUCP will keep survival below one percent (Figure 1).

Meanwhile, the prognosis for wild fall-run smolts under the TUCP is grim as they began moving through the Delta in late April and early May (Figures 2 and 3).  The extra month of normal outflow needed to help the salmon get to the ocean would amount to about 100-150 TAF, less than 10% of what is being supplied to water users from reservoirs in spring 2022.  Is the TUCP allocation to outflow and fish reasonable?

Figure 1. Fall-run salmon adult returns to the American River hatchery from Bay releases vs Delta outflow to Bay at time of release. Years noted are percent returns for below normal years 2016 and 2018, and wet year 2017 under normal rules. Blue dots with outflow below 5000 cfs are from 2014 and 2015, TUCP years. Red line is hypothesized relationship. Returns under normal rules are approximately triple the returns under TUCP rules.

Figure 2. Red circle denotes wild fall-run and spring-run smolts passing through the Delta in late April and early May 2022.

Figure 3. Peak migration of fall-run and spring-run smolts into Bay from Delta in late April and early May 2022.

2022 Sacramento River Operations – Temperature Management Plan

So much is at stake in this water year 2022: water supplies, water quality, agricultural production, hydropower production, as well as the future of salmon, steelhead, sturgeon, smelt, and other native fishes of the Klamath and Sacramento-San Joaquin watersheds. Despite the lessons of the 1976-1977, 1987-1992, 2007-2009, and 2013-2015 droughts, the choices and tradeoffs are more difficult, and effects more significant and consequential to the fish, in 2022, the third year of the 2020-2022 drought. The State Water Resources Control Board is about to approve 2022 water operation plans for Central Valley Project (CVP) and the State Water Project (SWP). Among the most immediate effects of these plans will be the fate of iconic fisheries resources of the Sacramento and Klamath Rivers, in 2022 and beyond.

The two key elements of the plans are (1) the Sacramento River Temperature Management Plan (TMP) governing Shasta/Trinity operations, and (2) the Temporary Urgency Change Petition (TUCP) governing Delta operations. A 4/5/22 post covered some aspects of the TUCP on Delta operations, which serves to cut demands on federal and state reservoir storage in the Sacramento River watershed by lowering Delta outflow requirements. (See also CSPA and allied organizations’ protest and objection to the TUCP.)

This post covers the 2022 TMP, which focuses on Shasta/Trinity storage releases and management of Shasta Reservoir’s storage releases and cold-water pool in support of Sacramento River salmon. It starts with a review of both the hydrological and biological effects of Shasta and Trinity operations in 2021. Starting with 2021 creates context in two ways. First, it explains the severe depletion of CVP and SWP storage in 2021, which created the avoidable portion of the extreme storage conditions of 2022. Second, it describes the disastrous failure to protect fish in 2021, both as consequence of bad management and contributor to the dire conditions of fisheries in 2022.

2021 Sacramento River Operations

The predominant characteristic of 2021’s operations of Shasta Reservoir and the Sacramento River was excessive reservoir storage releases over the spring and summer for water deliveries. Within this constrained context, the dominant biological features in 2021 were management of the cold-water pool for salmon , along with associated “downstream” effects on the lower river and Bay-Delta. The 2021 Sacramento River operations plan led to significantly reduced production in brood year 2021 of all four runs of Sacramento salmon.

I have divided the 2021 story into five event periods (Figure 1), each with differing conditions and outcomes:

Period A: The early-April through early-June period was characterized by rapidly rising high releases (6000-9000 cfs) for water deliveries in late April and May. Reclamation claimed it saved 300 TAF of Shasta’s cold-water pool using power bypass of warm surface water for the high spring releases. In reality, the excessive delivery of irrigation water unnecessarily depleted total Shasta storage by nearly 500 TAF and depleted the cold-water pool by 200 TAF. Those storage losses also crippled any ability to subsequently sustain the cold-water pool through the summer.

The releases of unseasonably warmer water (56-60ºF) also (as planned) inhibited spawning in the late-April to early-June portion of the winter-run salmon spawning season (about half of the historical season). It also stressed winter-run and spring-run adults in their upper river pre-spawn holding areas. Recent scientific studies suggest that such stress (extended holding and warmer water) may have contributed to thiamine deficiencies in spawners that contributed to poor subsequent fry survival and smolt production. Rapidly rising flows and water temperatures may have also compromised late-fall-run salmon egg incubation that normally continues into April. Irrigation deliveries in the middle and upper river led to lower flows and high water temperatures in the lower river (Figures 2 and 3); this both reduced the survival of emigrating spring smolts of all four races of salmon, and hindered and stressed upstream migrating winter-run and spring-run adults.

Period B: The mid-June period of cold-water releases (53-55ºF) was designed to stimulate winter-run adult spawning. It also provided 8000 cfs irrigation releases that unnecessarily depleted total storage and the cold-water pool by 6-8 TAF per day for nearly two weeks (~100 TAF lost cold-water pool and total storage). It also resulted in salmon spawning at 8000 cfs, spawning habitat conditions that led to water surface elevations that increased by one-foot and then dropped by two-feet over the summer salmon egg incubation season. I have not assessed the role of flow on the amount of quality spawning habitat available or on the potential of redd dewatering/stranding, although such factors should also be considered in evaluating an operations plan. Irrigation deliveries in the middle and upper river led to lower flows and high water temperatures in the lower river (see Figures 2 and 3), hindering and stressing winter-run and spring-run adults that were late in migrating upstream.

Period C: The late-June to early-August period was the main winter-run egg incubation period under 2021 operations. Flow releases increased to accommodate irrigation demands. Irrigation diversions, in turn, reduced flows in the river further downstream, leading to high water temperatures (72-78ºF) that blocked early arriving fall-run adult immigrants. A rise of almost two feet in water level in early June from the increased flow likely caused some redd scouring in the upper river spawning reach below Keswick Dam.

Period D: The mid-August to mid-September period was characterized by falling storage releases, associated declining water levels, and warming water as the cold-water pool and access to it declined. Winter-run egg incubation continued through the period and likely suffered from stressful water temperatures and redd dewatering. Flows in the lower river increased, and water temperatures declined, becoming less stressful for upstream migrating adult fall-run.

Period E: The late-September through November period was characterized by continued warming of water temperatures due to lessening access to Shasta’s severely depleted cold-water pool, followed by natural fall cooling. Releases and water levels declined rapidly in the spawning reach. At the beginning of the period, warm water interrupted or delayed spring-run and fall-run spawning, while a water level drop of several feet led to redd dewatering and stranding. Winter-run fry were also subjected to potential stranding during the drop in water level. Spring-run and fall-run spawning was likely hindered or delayed into November due to high water temperatures and decreasing flows and associated water levels.

The 2022 Plan

The May 2 2022 Final TMP Is a radical change from the 2021 plan and actual operations. For the first time, Reclamation has prioritized protection of fish over irrigation deliveries to senior Sacramento River Settlement Contractors. The changes also reflect the much lower available storage in this third year of drought (Figure 4). Water release projections are much lower to sustain the cold-water pool and cool downstream temperatures through the summer (Tables 1 and 2).

April Operations and Effects

April operations closely followed the draft plan that Reclamation submitted to the State Water Board on April 6. April operations using middle TCD gates and small imports of Trinity River water maintained Keswick releases at 52-53ºC and 3250 cfs per the draft 2022 TMP. Such operation helped preserve Shasta storage and the volume of the deeper, cold-water pool (<50ºF). Valley-wide precipitation since mid-April increased flows in the middle and lower Sacramento River, stimulating juvenile salmon emigration and adult spring-run and winter-run salmon immigration. A small pulse flow from Keswick to the 30 miles of spawning and rearing habitat below Keswick Dam would have helped stimulate and benefit these salmon migrations, especially those from the upper 30-mile reach that saw little or no benefits from the April storms, but this did not occur.

The draft TMP (April 6) had the same proposed releases from Keswick Reservoir as the final TMP (May 2). However, the end-of-September storage in Shasta Reservoir predicted in the final TMP (1135 TAF) is over 100 TAF lower than was the prediction in the draft TMP (1250 TAF).

Proposed May Operations

The proposed May 4500 cfs release would come from Shasta Dam’s middle gates with access to warmer surface water in the lake, thus saving some of the cold-water pool. Such savings would require warmer releases that would delay spawning and stress holding adult winter-run and spring-run salmon.

For those winter-run who do spawn in May, egg survival could be compromised by the warmer water. With warming surface waters and warmer reservoir inflows in May, and more pre-spawn adult salmon arriving in the 10-mile spawning reach below Keswick Dam, a Keswick release temperature maintained at or below 51ºF would ensure the 10-mile spawning and holding reach is maintained near 53ºF. A colder release would require proportionately more cold water be released from deeper dam gates.

In reality, middle gate operation through early May (Figures 5 and 6) has sustained cooler-than-expected daily-average release temperatures at 51-52ºF. Hydropower peaking has accessed the warmer upper layers of the reservoir (Figures 7 and 8), saving some of the cold-water pool as planned. However, middle-gate operation under hydropower peaking, and gradual warming of reservoir surface waters, will result in increasing release temperatures per the plan later in May. A rapidly warming reservoir may necessitate use of lower gates or less hydropower peaking operations to maintain <54ºF through May per the plan. If spawning commences in early May due to cooler than planned dam releases, higher late May release temperatures would begin to compromise earlier-spawned egg survival. This should cause some re-evaluation of the plan.

Proposed June-September Operations

The proposed June-September 4500 cfs release (4000 cfs in September) from Shasta Dam will be from the lower TCD gates from the cold-water pool at ~50ºF (Table 2). Slightly higher Keswick Dam release water temperatures are predicted due to warming in Keswick Reservoir at ~4500 cfs through-flow. Water temperatures 5 miles downstream at Highway 44 will increase slightly more due to warm air temperatures.

The final temperature management strategy, based on recommendations received from the Sacramento River Temperature Task Group (SRTTG), is to target 58ºF at Highway 44 during the initial part of the season and then target 54.5ºF for 16 weeks around the estimated peak spawning date of Aug 2. This would result in targeting 54.5ºF from June 7 through September 27 or until the cold water is used up. Due to the limited available control in operating the middle gates (as described above), temperatures in June and July may be cooler than 54.5ºF. Reclamation will operate the TCD to target as close as possible to 54.5ºF to conserve cold water for maintaining target temperatures throughout the critical period.

Reclamation also received feedback from SRTTG members that an initial target of 58ºF would help to conserve cold water for later during the more critical portion of the temperature management season. The problem with this is that it will delay spawning, stressing yet-to-spawn adults and compromising survival of earlier-spawned embryos.

Fall Operations

Fall operations will be similar to those described above for Period E in 2021, with the exception of a lesser drop in flow. Water temperatures in late summer and fall will increase as the cold-water pool is depleted and access to it ends. Increasing temperatures will delay spring-run and fall-run spawning and stress pre-spawn adults (potentially aggravating the thiamine deficiency problem).

Uncertainties

The planners have noted significant uncertainties that will require intensive real-time operations and management throughout the summer to achieve the various goals and targets throughout the system. To address uncertainty, Reclamation has employed conservative estimates of future conditions in the modeling assumptions (e.g., hydrology, operations, and meteorology) and projections, and has included as part of the TMP the potential to make changes, in consultation with the SRTTG, Water Operations Management Team, and/or the Shasta Planning Group. The State Board and NMFS should be included in the decision process.

Infrastructure limitations

The 2022 TMP was developed in consideration of the limitations on using the TCD and the need for temperatures below 56ºF at the Livingston Stone National Fish Hatchery. Efforts to address these limitations should be accelerated. Hydropower peaking operations changes should also be considered.

Related Actions to the Final 2022 TMP

1. Six-Fold Increase in Winter-Run Hatchery Smolt Production
Reclamation plans to fund a six-fold increase in the production of hatchery winter-run smolts this year with staged fall-winter releases from the hatchery and Battle Creek. Such releases should timed to coincide with natural flow pulses and pulse flows from Keswick Dam.

2. Transfers of Adult Salmon
The plan includes the capture and transport of adult winter-run salmon to the headwaters of Battle Creek. Good additional measures would be to give these adult fish thiamine injections and to enhance spawning gravels in Battle Creek as soon as possible.

3. Thiamine Treatments
Stresses imposed prior to spawning (e.g., delayed spawning, low flows, warm water during migration) and holding contributes to thiamine deficiency and high mortality of yolk sac fry, both in hatcheries and wild salmon1. Only hatchery salmon can be treated effectively at adult or egg stage, so efforts should be made to treat any wild adults that are handled, as well as to minimize pre-spawning stresses (e.g., erratic flows and high water temperatures).

4. Water delivery cut to 18% to Settlement Contractors
The TMP proposes to limit water deliveries to Sacramento River Settlement Contractors to 18% of their contracted amounts. The State Board should enforce this limitation. Reclamation should subordinate the timing of water releases to contractors to the needs of salmon downstream of Keswick Dam.

5. Reduced Downstream Deliveries
Demand on Shasta storage for Delta inflow/outflow has been reduced by relying more on other SWP/CVP and non-project reservoirs. However, lower Sacramento River and Delta inflows have reached water temperatures above 65ºF in early May, which puts additional stress on salmon that are immigrating in late spring. It is not a question of whether in May or June lower river water temperatures will exceed 68ºF – the state standard – but when.

6. System-Wide Water Management
Reclamation plans to manage system water supplies to minimize demands on Shasta’s cold-water supply. The Plan and temperature modeling relies on numerous drought actions throughout the Sacramento watershed to reduce reliance on stored water from CVP and SWP reservoirs this summer. “These drought actions have added a degree of flexibility to manage storage at Shasta, Oroville and Folsom reservoirs for meeting public health and safety needs, repelling salinity in the Delta, producing hydropower and providing additional cold water for fishery protection throughout the summer.” In 2022, Reclamation has finally cut deliveries to Sacramento River Settlement Contractors substantially below minimum amounts stated in contracts, in order to protect salmon. However, DWR has not done so for Feather River Settlement Contractors. Reclamation and DWR should be looking at system-wide delivery reductions. Reclamation should also call on New Melones for Delta salinity control as needed. See also NRDC et al. Objection to the TMP (May 6, 2022) for additional recommended system measures.

7. Real-Time Adjustments and Reporting
“Daily releases may vary from these flows to adjust for real-time operations. 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.” Reporting, scrutiny, and decision making should be open processes.

8. Restoration of Salmon Upstream of Dams
Reclamation is committed to restoring endangered salmon to their historical habitat upstream of Central Valley rim dams. This program should be accelerated.

Tables 1 and 2 are copied directly from the Final TMP dated May 2, 2022.

Figure 1. Keswick Dam release water release rate and temperature, April-November 2021. Five general periods (A-E) are depicted, based on flow-temperature conditions as described in more detail in text. A. Spring high storage release rate (6-9K cfs), including extensive power bypass releases of warm surface water. B. A late-June cold water release to stimulate winter-run salmon spawning (<53ºF). C. A post-spawn higher irrigation release period with late-egg-stage sustaining water temperatures. D. Cold-water pool saving period with falling flows and higher water temperatures. E. Early fall period with loss of access to cold-water pool and reduction in storage releases.

Figure 2. April-December 2021 Sacramento River flow below Keswick Dam (river mile 300) and below Wilkins Slough (river mile 120). The difference between the two locations, plus tributary and ag return inputs, equals total irrigation deliveries via surface diversions and ground water depletions.

Figure 3. Water temperature in the lower Sacramento River at Wilkins Slough (river mile 120) May-August 2021, along with average for past 13 years. Note that the state’s year-round water quality standard for the lower Sacramento River is for water temperature to remain below 68ºF. Water temperatures above 65ºF are stressful to migrating juvenile and adult salmon. Water temperatures above 70ºF hinder adult salmon migration. Water temperatures above 75ºF are lethal to salmon.

Figure 4. Shasta Reservoir storage in 2022 and other selected years.

Figure 5. Shasta Reservoir water temperature profile at end of April 2022.

Figure 6. Water temperatures of Shasta and Keswick Dam releases in 2021 and to date in 2022.

Figure 7. Hourly water temperature in Shasta Dam releases, 4/27-5/7 2022.

Figure 8. Hourly Shasta Dam flow releases 4/27-5/7 2022.

  1. Adult salmon thiamine stores reduce most during the pre-spawning fast (Vuorinen et al. 2020).  Vuorinen PJ, Rokka M, Ritvanen T, Käkelä R, Nikonen S, Pakarinen T, Keinänen M. 2020. Changes in thiamine concentrations, fatty acid composition, and some other lipid-related biochemical indices in Baltic Sea Atlantic salmon (Salmo salar) during the spawning run and pre-spawning fasting. Helgol Mar Res. 74(1):1–24. doi:https://doi.org/10.1186/s10152-020-00542-9. (Crossref), (Web of Science ®), (Google Scholar) https://hmr.biomedcentral.com/articles/10.1186/s10152-020-00542-9