Category Archives: Chinook Salmon

Wild Salmon Sanctuaries

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In a 2014 blog post, Peter Moyle wrote about the Blue Creek Salmon Sanctuary on a large tributary of the lower Klamath River.  The Blue Creek effort is one of the most important initiatives toward saving salmon in California, and also serves as a demonstration and an inspiration.  California needs more salmon sanctuaries to preserve the state’s wild salmon heritage.

There are many potential salmon sanctuaries throughout California.  In this post, I list highly recommended rivers plus and few new ones.  I include only those I personally know well, but there are likely more that fit the paradigm.

My suggestions come from two major watersheds that deserve special mention and attention.

Klamath River Watershed:

 The Salmon River is a wild, natural tributary of the lower Klamath River that retains the last wild population of endangered spring-run Chinook salmon. Its watershed now suffers from the ravages of recent forest fires.  The river is a special place to the Karuk Tribe.

  • The Scott River, the eastern neighbor to the Salmon River, features the last significant wild population of Coho salmon in California. While nearly ruined by logging, fires, and ranch development, the Coho hang on almost belligerently with the help of the Trinity and Marble Mountains and from some of the ranching community.  The river begs for the return of its beaver, so it can again be called “Beaver Valley.”  Some of the ranchers deserve credit for keeping the river and its fish on life-support.
  • The Shasta River is the next neighbor to the east of the Scott River. The river sustains the Klamath’s largest population of wild fall-run Chinook salmon, thanks in large part to the efforts of the Nature Conservancy.  The river has hope for the return of the Coho salmon with the help of ranchers, Sierra Pacific Industries, the tribes, and Crystal Geyser.  Ranchers, please no more revolts.
  • Deming Creek, among the headwaters of the Sprague River, a major Klamath River tributary in Oregon that drains into California, is a historical remnant of a creek that once supported wild spawning Klamath spring-run salmon and steelhead (really). It still has the southernmost extant population of endangered bull trout, which once occurred in California but are now extirpated in this state.  If the Klamath dams are removed, will the salmon return to Deming Creek?  I suspect the salmon will need some help getting to this beautiful place.

Sacramento River Watershed:

  •  The upper McCloud River above and below McCloud Falls is one of the most beautiful places in California. The McCloud once sustained winter-run and spring-run salmon below the falls.  Above the falls on the south flank of Mt. Shasta is the McCloud Redband Trout Refuge.  If part of the strategy is for trap-and-haul sanctuaries, this is a great place to put winter-run or spring-run salmon.
  • Upper Mill Creek and Deer Creek on the south flank of Mt. Lassen are two gems that retain small populations of spring-run Chinook salmon at the highest elevations known for the species.  Ravaged by fires in recent years, they too need help.  At least salmon in theses streams do not need a taxi service.
  • To the south of Deer and Mill creeks, Butte Meadows on upper Butte Creek upstream of falls and water diversions has much potential as a sanctuary. This location needs a taxi service only for adult spawners, but not their offspring should be able to migrate downstream volitionally.
  • Upstream of Lake Almanor, the upper North Fork Feather River drains the southern flank of Mt. Lassen, eventually finding its way past a series of dams into the Central Valley and the Sacramento River. This is another trap-and-haul sanctuary with strong potential, though it was severely affected by the recent Dixie Fire.
  • The upper North Yuba River above Bullards Bar Reservoir is a gem of a stream that once supported spring-run Chinook salmon. Again, this would be a trap-and-haul option.
  • The Middle Fork American River well upstream of Folsom Reservoir, another historical spring-run salmon stronghold, is also a good candidate. Badly damaged in the 2022 Mosquito Fire, the Middle Fork American is in need both of help with the forest and of a two-way taxi service for reintroduced salmon.

One thing common to many of these potential sanctuary locations is a legacy of massive fires in recent years.  A substantial effort is needed to restore these Klamath-Trinity and Sierra ecosystems to make them sustainable once again for California salmon and steelhead.

I also advocate for Chinook salmon sanctuaries below all our major Central Valley rim dams.  The dams were built with the promise of mitigation for the salmon runs.  It is time these many-decades-old promises were kept.   Though most of the lower rivers have escaped the direct ravages of fire, the consequences to their upper watersheds still affect the Valley reaches.  Without the remnant Valley salmon, there would be few salmon left in California.

Time has taken a toll on the Valley salmon below the rim dams.  To weather the effects of droughts, fires, and climate change, and to restore viable populations in the major salmon-bearing rivers, sanctuaries in both the upper watersheds above the dams and downstream of the dams are necessary.

For more information on California’s Chinook salmon see: https://wildlife.ca.gov/Conservation/Fishes/Chinook-Salmon

San Joaquin Salmon Population Status – End of 2021

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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.

 

Update on Shasta River – Summer 2022

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In a post in July 2021, I discussed the problems facing Shasta River salmon.  An 8/20/22 article in CalMatters described how the problems became acute this summer when the local ranchers’ water association ignored the State’s emergency order to stop diverting water from the Shasta River in this drought year.  After complying for most of the summer, the ranchers diverted about 20 cfs of water for about a week in mid-August (Figure 1; blue line)

Figure 1. Streamflow in the lower Shasta River upstream of Montague. Ranchers complied with the State’s emergency drought order until mid August. After a week under the threat of fines they stopped diverting.

What the ranchers did in mid-August was simply what they had been doing for decades but were asked to stop in 2022 (see Figure 1, median for 37 years; orange line).

It appears based on the downstream Yreka gage that other ranchers also took part in ignoring the State’s mandate (Figure 2) as the deficit reached about 30 cfs.  These other diverters also returned to compliance with the mandate after a week of non-compliance.

Several reductions in Shasta River flow are not mentioned in the CalMatters article. The total water supply to the Shasta River from springs  originating from Mt. Shasta is somewhere between 250 and 300 cfs in most summers (Figure 3 shows summer of wet year 2017).  In critical drought year 2022, the total supply is closer to 200 cfs, because there are less spring inputs and demands are greater.  In general, about 40-50 cfs is taken out by large wells from the 100 cfs input of Big Springs (leaving the roughly 50 cfs of river flow reaching Montague in Figure 1).  The springs shown in Figure 3 provided less inflow in drought year 2022 than they did in 2017, because Lake Shastina is critically low and input from the upper river and its springs are lower (Figure 4).  The upper Shasta River also loses water at Weed to the city supply and to water bottlers.

Coho salmon once thrived in the Shasta River below Big Springs and in the upper Shasta River.  Coho have suffered for many decades under the historical pattern shown in Figures 1-3.  Some of the remnant population may have been living in the 20 miles of river below Montague this summer, until they were subjected to the low flows and very stressful water temperatures that came with the one week of unauthorized diversions.  There is also this year’s run of fall-run Chinook salmon holding in the Klamath River at the mouth of the Shasta River, awaiting sufficient flow and adequate water temperatures to migrate up the Shasta River.

The fact is that the State Water Board can’t solve a century-old problem with an emergency decree in one dry summer.  The State needs to develop a comprehensive solution for the Shasta River that provides 50 cfs of water for salmon year-round (at Montague Figure 1, and Yreka, Figure 2), out of the available 200-300 cfs supply.  Users need to share the rest equitably, especially in a drought year like 2022.

Figure 2. Streamflow in the lower Shasta River downstream of Yreka in the summer of 2022. Also shown is daily average mean flow for the previous 85 years.

Figure 3. Selected Shasta River hydrology in late May of wet year 2017. Roughly 150 cfs of the 300 cfs total basin inflow in this wet year is being diverted for agriculture, city water supply, and water bottling (Weed) with remainder reaches the Klamath River. Red numbers are larger diversions. The “X’s” denote major springs. Big Springs alone provides near 100 cfs. Of the roughly 100 cfs entering Lake Shastina (Dwinnell Reservoir) from Parks Creek and the upper Shasta River and its tributaries, only 16 cfs is released to the lower river below the dam. The remainder is stored and released to east-side irrigation canal (about 50 cfs). Red numbers and arrows indicate larger agricultural diversions. Up to 15 cfs is diverted to the upper Shasta River from the north fork of the Sacramento River, west of Mount Shasta. Blue dots show locations of river flow gages.

Figure 4. Hourly flow in the upper Shasta River in summer 2022 at Edgewood just downstream of the City of Weed.

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

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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

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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.