Yuba River Fall Run Salmon – Status Winter 2023

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

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

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

Graph from 1953 though 2021

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

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

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

Graph of Spawners versus Recruits

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

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

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

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

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

Two graphs

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

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

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

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

Graph water temprature versus time

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

Graph of water temperature versus time

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

Graph of Daily Discharge in 2014

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

Discharge Graph 2014

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

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

Graph of discharge in 2015

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

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

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

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

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

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

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

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


San Joaquin Salmon Population Status – End of 2021

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

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

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

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

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

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

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

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

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

Grandtab Table

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

Bar chart from Grandtab data

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

Stacked Barchart Grandab Data

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

Pie chart rmpc.prg data

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

Line graph USGS data

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

Line chart USGS data

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

Pie chart rmpc.org data

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

Line graph and map

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


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

The Delta in April-June 2022 under TUCP

A lot has been said about the drought’s effect on water supplies for cities and farms, but little is said about how Delta fish are faring.  Freshwater inflow to the Delta was about half of normal in April through June 2022 because of the State Water Board Order approving the Department of Water Resources (DWR) and the Bureau of Reclamation’s Temporary Urgency Change Petition  (TUCP) for Delta operations.  With some of this limited Delta inflow going to water users during April, May and June, little was going to the fish.

The State Water Board granted the TUCP because Central Valley reservoir storage was so low at the end of winter in this third year of drought.  During drought, most of the Delta’s late spring and summer inflow comes from releases from storage in Shasta, Oroville, and Folsom reservoirs.

The TUCP has ended, and the normal operating rules for the Delta under Water Rights Decision 1641 have gone back into effect as of July 1.  It is now a good moment to review the effects of this most recent TUCP.

Conditions Under TUCP (April-June 2022)

Delta inflow from the Sacramento River and tributaries averaged about 7500 cfs while the TUCP was in effect (Figure 1).  Releases from Folsom Reservoir averaged 1000-2000 cfs of this inflow.  Releases from Oroville Reservoir varied widely, but averaged about 2500 cfs over the period.  Other inflow came from the Sacramento River (Shasta Reservoir) and its tributaries, which during the TUCP period averaged about 3000-4000 cfs.  The San Joaquin River and its tributaries contributed on average another 1000 cfs to Delta inflow.

There are three main uses of Delta inflow when inflow is low: repelling salt water, south Delta exports, and in-Delta use.  South Delta exports were about 1300 cfs while the TUCP was in effect.  Delta outflow, holding back the salt water, required roughly 4000 or more depending on tides.  Net in-delta use (water diversions other than south Delta exports) accounted for the rest.

Salinity (EC, mS/cm) at Emmaton (west Delta Figure 2) , normally kept near 500 per the state standard for agriculture, increased to levels ranging from 500 to 8000 (Figure 2), with daily average of 2000 to 4000, four to eight times the standard.

At Jersey Point, where the standard is 450-750 EC, salinity ranged from 1200 to 2300 in June (Figure 3).

Conditions After TUCP (Early July 2022)

After the TUCP expired, conditions changed as regulatory requirements returned requirements under Decision 1641.  Delta inflow increased to 12,500 cfs (Figure 1).  At this date, salinity has fallen toward the appropriate salinity standards (Figures 3 and 4).

What does this mean for the Delta and its Fish? 

  1. The agricultural salinity standard of 500 mmhos at Emmaton near Sherman Island in the Sacramento River channel was “relaxed” under the TUCP (Figure 3). Salt water was able to push further upstream and mix to a further extent with inflow.  The daily salinity (EC) range of approximately 500-8500 mmhos, an increased level of spring salinity not seen since the 2014 and 2015 drought under earlier TUCPs.
  2. Likewise, the average daily salinity (EC) standard at Jersey Point near Sherman Island in the San Joaquin River channel (Figure 4) was also not being met.
  3. Salinity was managed under the TUCP to meet the minimum drinking water standards (<800 mmhos) near municipal water supply diversions in the central Delta (Figure 5). (I would not drink this water or put it on plants.)
  4. Throughout June, net flows in the Old and Middle River channels in the central Delta were southward toward the South Delta export pumps (Figures 2 and 6).
  5. While the TUCP was in effect, salt water moved upstream in the Sacramento River channel near Rio Vista and into Cache Slough (Figure 7). Within the Cache Slough Complex, water moved upstream (Figure 8) in part due to water diversions in the north Delta.
  6. Delta inflows from the Sacramento River at Freeport fell below 10,000 cfs from April through June 2022 as allowed under the TUCP (Figure 1). This drop led to the increases in salinity noted in Figures 2-8.
  7. Low Delta inflows also contributed to higher water temperatures throughout the Delta during and after the TUCP period (Figures 9 and 10). Water temperatures above 72 degrees are detrimental to most of the native Delta fish.


  • The TUCP allowed reduced Delta inflows that preserved some reservoir storage in critical drought year 2022.
  • Inflows dropped below the normal 10,000-12,000 range that keep Delta salinity at Emmaton and Jersey Pt below the 500 mmhos agricultural salinity standard.
  • Central and north Delta water diversions from the Delta’s pool of freshwater contributed to upstream movement and loss in quality and quantity of the low-salinity zone, a critical nursery habitat of Delta native fishes.
  • The shift in the location of these important habitats into the north and central Delta, and the associated warming from the more-eastward position and lower net flows represent a serious impact on Delta native fishes including Delta smelt, longfin smelt, green and white sturgeon, winter-run, fall-run, and spring-run salmon, and steelhead, which use these habitats through the spring and summer for rearing and migration.

Figure 1. Delta inflow (cfs) from the Sacramento River as measured at Freeport in 2022. Note the TUCP allows streamflow at Freeport to be reduced below the 10,000-12,000 cfs range that is normally necessary to meet Delta salinity standards at Emmaton and Jersey Pt.

Figure 2. West Delta salinity gage locations with net flow direction during TUCP period April-June 2022.

Figure 3. Salinity (EC) range at Emmaton in west Delta in 2022.

Figure 4. Salinity (EC) at Jersey Point in west Delta in 2022.

Figure 5. Salinity (EC) in the central Delta in Old River channel in 2022.

Figure 6. Net flows in central Delta Old River and Middle River channels in 2022.

Figure 7. Salinity (EC) in Cache Slough channel of north Delta near Rio Vista in 2022.

Figure 8. Net flows in Cache Slough near Liberty Island in 2022.

Figure 9. Water temperature of the Sacramento River near Freeport in 2022.

Figure 10. Water temperatures in the Delta and Delta inflows May-July 2022.

EMM – Emmaton on the Sacramento River channel in west Delta.

WLK – Lower Sacramento River below Wilkins Slough above the mouth of the Feather River.

PPT – Prisoners Pt in the central Delta channel of the San Joaquin River.

DLC – Sacramento River channel in the north Delta at the Delta Cross Channel.

OBI – Old River in central Delta.

RVB – Rio Vista Bridge in west Delta channel of the Sacramento River.

SJJ – San Joaquin channel in west Delta at Jersey Pt.

OH4 – Old River in central Delta.

ANH – San Joaquin River channel of west Delta at Antioch.

MSD – San Joaquin River channel at entrance to Delta at Mossdale.

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.