Another Threat to Winter-Run Salmon in 2021 – Fall Sacramento River Bypass Overflows

Record late-October Valley rainfall brought Sacramento River flows high enough to overflow into the Tisdale Bypass (Figures 1 and 2).  Such early-fall overflows are highly unusual (Figure 3). The sudden surge filled nearly 30 square miles of the Sutter Bypass before exiting to the south, back to the Sacramento River (Figure 4).  Bypass channels rose 6-10 feet during the storm, with the help of tributary inflows (CDEC gage data not shown), flooding much of the agricultural fields, levee borrow pits, duck club ponds, and natural wetlands and ponds of the Sutter Bypass.

Riding the wave of river flow were juvenile winter-run salmon moving down the Sacramento River (Figure 5).  Many spilled over the weir into the Bypass and into flooded habitats.

After the storms, a sudden drop in flow quickly drained the Sutter Bypass, and many juvenile salmon became stranded in ponds and fields of the Bypass floodplain.  The problem with the short-lived early fall flooding is that stranded habitats dry up or become too warm too sustain the young salmon through the fall, winter, or even spring (if the Bypass does not flood again).  Predation by abundant non-native predatory fish in the Bypass is another problem, especially as the high flows of muddy water retreat.

Also at issue is the attraction of upstream migrant adult fall run-salmon into the Bypass.  Such salmon get trapped downstream of the Tisdale Weir.  The Tisdale Weir Rehabilitation and Fish Passage Project is supposed to mitigate this situation.  But it is only in the planning and design stages, and until that project is complete, adult salmon will continue to be trapped below Tisdale Weir.  In addition, the Tisdale Weir project “does not analyze the impacts to additional special status fish (juvenile salmonids) being attracted into bypass from extended days of inundation and subsequently being stranded without adequate drainage or a plan to mitigate for that.” (Project EIR).  The Tisdale Weir project also needs to plan for and mitigate the juvenile stranding in the Sutter Bypass.

Until the Tisdale Weir Project addresses these issues, fall spills into the Sutter Bypass from flood control weirs on the Sacramento River will reduce survival of winter-run salmon and other anadromous salmonids of the Sacramento River and its tributaries.

Figure 1. The Tisdale Weir and Bypass from the Sacramento River to the Sutter flood bypass.

Figure 2. Overflow (cfs) into the Tisdale Bypass from the Sacramento River 10/24-26/2021. Data Source: CDEC.

Figure 3. Tisdale Weir overflows 1998-2019.

Figure 4. Sutter Bypass properties subject to flooding from Tisdale Weir overflow.

Figure 5. Juvenile salmon collection in screw traps in Sacramento River near Tisdale Weir Aug-Nov 2021.

 

 

Feather River Salmon Recovery Responsibilities, Commitments, and Recommendations

The State Water Project (SWP) is not protecting salmon in the Feather River.  The Feather River’s once-prolific populations of wild spring-run and fall-run salmon have been replaced by smaller numbers of hatchery fish of inferior genetic composition.

The fact that the replacement of wild fish by hatchery fish plagues all salmon stocks in the Central Valley Evolutionarily Significant Units (ESUs) is no excuse.  The California Department of Water Resources (DWR) has many responsibilities and commitments to protect Feather River salmon under the SWP’s project’s hydropower license, water rights, and other permits, and more generally under the public trust doctrine and the reasonable use doctrine in the state constitution (Article X, Section 2).  The SWP has not met these responsibilities or related commitments since the SWP’s completion in the 1960s.

Neither Feather River nor Central Valley salmon recovery can be achieved without cleaning up the mess in the lower Feather River.  This fact is recognized widely in salmon recovery plans, federal biological opinions, State incidental take permits, and even in part in the Oroville Settlement Agreement for the relicensing of the SWP’s hydroelectric facilities at Oroville.  DWR has made many promises and commitments toward salmon recovery, but has realized very few.  While DWR has spent billions on upgrading project infrastructure, especially after the 2017 spillway failure, it has spent little toward salmon recovery.

So how should DWR focus its salmon recovery process for the Feather River at this point?

Well, most certainly on mandatory provisions in the soon-to-be issued FERC hydropower license and related State Board water quality certification.  Also, on existing or needed conditions in its water right permits that extend beyond the small geographic scope of the FERC license.  The next focus should be on  the “Habitat Expansion Agreement for Central Valley Spring-Run Chinook Salmon and California Central Valley Steelhead” (HEA) that DWR and Pacific Gas and Electric Company (PG&E) agreed to during the Oroville relicensing.1 There are also requirements in the Reasonable and Prudent Measures in the 2016 federal biological opinion for the Oroville relicensing.

The overall focus should be on recommendations in specific salmon recovery plans pertaining to the project.

Below are my recommendations for top priority actions for Feather River salmon recovery from among the sources mentioned above.

Spring-Run and Fall-Run Salmon Introgression

A primary focus and priority should be on minimizing introgression of the spring-run and fall-run salmon populations in the hatchery and natural spawning area of the 8-mile Low Flow Channel (LFC) downstream of Oroville Dam.

For the natural spawning area of the LFC, one option is a segregation weir at the lower end above the Thermalito Afterbay outlet that would provide for selective passage of selected adult spawners into the spawning area.  Similar weir systems are operated in lower Battle Creek and lower Butte Creek.  For example, the weir could provide seasonal passage to accommodate only spring-run spawners that arrive earlier than fall-run.  The fall-run would be forced to spawn downstream of the afterbay outlet in the High Flow Channel (HFC) where habitat conditions, especially water temperatures, would be more suitable later in the year when fall-run salmon are spawning.  The weir could also trap fish to allow direct segregation or egg taking, or trapping-and-hauling of selected adults or offspring produced in the LFC.

The hatchery program should focus on broodstock selection and hatchery operations that produce returning adult spring-run and fall-run salmon of the highest genetic integrity possible.   It should also operate to limit straying of Feather River origin hatchery salmon.  Hatchery operations should also focus on strategies for smolt releases that provide the greatest return while limiting effects on wild salmon.  Otherwise, the Feather River Fish Hatchery Improvement Program (Article A107 of the Oroville Settlement Agreement) should be implemented.  This program sets specific targets for hatchery temperatures, requires development of a hatchery management program (including a Hatchery and Genetics Management Plan), potential installation of a water supply disinfection system, and funding for annual hatchery operations and maintenance.

Lower Feather River Habitat Improvements

There are many potential habitat improvements in the LFC and in the High Flow Channel (HFC, the lower Feather River downstream of the outlet of Thermalito Afterbay).  Habitat improvements could provide significant benefits to adult salmon holding and spawning success, and wild fry survival and smolt production.  One general category is water quality (i.e., water temperature) and streamflow management through improved infrastructure and operations strategies of flow releases to the LFC and HFC.  The second category is improvements to the physical (non-flow) habitat features, including channel configuration (depths, velocities, and substrate composition) in both the LFC and HFC.

Flow and Water Temperature

Adult spring-run salmon migrate in spring to the lower Feather River, then hold in deep pools over the summer to spawn in early fall.  Adequate flows and cool water temperatures are essential elements of (1) spring adult migration habitat in the lower Feather River and (2) over-summering holding habitat.  Without adequate flows for migration and holding, adult salmon are prone to disease and pre-spawn mortality, poor reproductive success, or lower survival of eggs.  Water temperatures should be no higher than 65oF during migration and 60oF during holding to minimize such detrimental effects.  Water temperatures in the HFC (or LFC) should not exceed 65oF in spring (Figure 1).  Water temperatures in the LFC should not exceed 60oF in summer (Figure 2).  The various planning documents outline potential options to reduce water temperatures in the LFC and HFC.  These include measures to sustain Oroville Reservoir’s cold-water pool and reliably release water from it.  They also include measures to keep water in the Afterbay complex cooler prior to release into the HFC.  Still other measures may include limiting release of water from the Afterbay through a variety of modifications to facilities and operations.

Physical Habitat Features

The Biological Opinion and Settlement Agreement for the Oroville relicensing include prescriptions for the restoration and enhancement of lower Feather River salmon habitat, consistent with the NMFS Salmon Recovery Plan:

  1. Design and build infrastructure and stream channel features that will allow for segregation and reproductive isolation between fall-run and spring-run Chinook salmon naturally spawning in the LFC of the Feather River.
  2. Develop a spawning gravel budget and introduction plan, and implement the plan.
  3. Design, construct, and maintain side-channel and off-channel habitats for spawning and rearing salmon and steelhead.
  4. Obtain river riparian and floodplain habitat through easements and/or land acquisition as needed, allowing the river room to grow and move as necessary to provide key transition habitats, and to minimize degradation (such as channel incisions/filling and substrate armoring) of existing high quality habitat features. Provide a balance between the needs of flood conveyance, recreation, and aquatic, riparian and floodplain habitat in and near an urban environment.
  5. Design, build, and maintain channel features that provide optimum habitat, fish passage, and flood control necessary to minimize scour and erosion. High-flow floodplain channels may be such a feature.
  6. Provide deeper holding habitat and cover for adult over-summering spring-run salmon in the channel habitat features described above. Such habitat is often larger pools with a large bubble curtain at the head, underwater rocky ledges, and shade cover throughout the day. Adult spring-run Chinook salmon may also seek cover in smaller “pocket” water behind large rocks in fast water runs.

Benefits to Other Species

Efforts to improve salmon habitat in the lower Feather River will benefit other important native fish.

The lower Feather River is home to other significant fisheries resources including the following:

  • Spawning anadromous steelhead – spawning is concentrated in Low Flow Channel below the Fish Barrier Dam in winter and spring.
  • Steelhead eggs in gravel redds are concentrated in Low Flow Channel below the Fish Barrier Dam in winter and spring.
  • Steelhead yearling smolts rearing occurs in the Low Flow Channel and the High Flow Channel in winter and spring.
  • Steelhead fry rearing occurs in the Low Flow Channel and the High Flow Channel in winter and spring.
  • Spawning of green and white sturgeon occurs in spring in the High Flow Channel.
  • Sturgeon eggs are found in rock crevices of the river bottom in the High Flow Channel in spring.
  • The newly hatched larvae and fry of sturgeon occur on the river bottom in the High Flow Channel in spring.
  • Resident trout and non-salmonid fish occur year-round throughout the lower Feather River.

Habitat Expansion Agreement – Final Habitat Expansion Plan

The Oroville Project Habitat Expansion Agreement (HEA) requires creation of habitat suitable to increase populations of Central Valley spring-run Chinook salmon by a minimum of 2000 adults.  The Habitat Expansion Plan proposed by DWR and Pacific Gas and Electric Company (PG&E) focuses on physical habitat improvements to the Lower Yuba River to benefit spring-run Chinook salmon.   According to DWR and PG&E, this would develop a viable, self-sustaining population of spring-run Chinook salmon below Englebright Dam.

In my opinion, this is a big mistake.  The lower Yuba River below Englebright Dam has many of the same problems as the lower Feather.  Its spawning habitat already has capacity for many more spring-run salmon than are currently utilizing it.

A much better option is saving the Butte Creek spring-run salmon, the largest core population of the CV Spring Run Salmon ESU.  A first phase of a Butte Creek recovery program would be to secure Butte Creek’s supply of cold Feather River water for the immediate future.  PG&Es decommissioning of the DeSabla-Centerville Hydroelectric Project would potentially eliminate or reduce cold-water inputs from the West Branch of the Feather River to Butte Creek.  The DeSabla Project moves water from the West Branch Feather in canals for release into Butte Creek through the DeSabla Powerhouse.  This additional, relatively cool water provides holding and spawning habitat that presently sustains Butte Creek’s spring-run salmon and supports Butte Creek’s fall-run salmon and steelhead.

A second phase of a Butte Creek recovery program would entail removal of the Lower Centerville Diversion Dam, a low-head dam on Butte Creek just downstream of the DeSabla powerhouse (Figure 3).  Since 2014, this dam has not diverted any water.  Removal of the dam and diversion, and potentially removal or modification of other fish passage improvements at natural barriers if needed, could allow access to many miles of upstream spawning and rearing habitat on Butte Creek.  This would truly expand spring-run habitat in the Central Valley.

Summary and Conclusion

Feather River salmon recovery should proceed through improvements in flow, water quality, and physical habitat, project operations and facilities, and hatchery operations and facilities.  Habitat expansion for spring-run salmon should focus on saving the existing run of spring-run salmon on Butte Creek and expanding their upstream range, not on physical improvements to the lower Yuba River.

Figure 1. Water temperature in the lower Feather River within the HFC in spring 2020 and 2021. Red line is upper water temperature safe limit for migrating salmon.

Figure 2. Water temperature in the lower Feather River within the LFC, 2013 and 2021. Red line is upper water temperature safe limit for pre-spawn, adult holding salmon.

Figure 3. Map of PG&E DeSabla Hydroelectric Project features on Butte Creek and the West Branch of the Feather River.

Preserving and Restoring Wild Salmon Populations while Sustaining Commercial and Sport Fisheries with Hatcheries

The Problem

Hatcheries bypass the high mortality life-history phases of wild salmon populations.  As a result, hatcheries contribute far greater salmon smolt production to the ocean per number of eggs than do wild populations.  Without hatcheries, the replacement rate of Central Valley salmon populations would be less than 1-to-1, and the populations would move toward extinction.  Without hatcheries, there would be no commercial or sport salmon fisheries in California today.

But hatcheries bring many real problems for wild salmon.  These problems include in-breeding/domestication, disease transmission, and over-harvest of, competition for, and direct and indirect predation on wild salmon populations.  In-breeding has already had dramatic effects on the salmon populations, leading to the loss or degradation of many important life-history traits and of subpopulations that carry these traits (the “Portfolio Effect”).

Having lost many traits that nature provided over millions of years of natural selection, hatchery salmon today are simply less able to cope with the new world they now face.  They mature younger and smaller.  They are less able to adapt to changes in their food supply.  They often can’t compete and are less able to avoid predators.  Many arrive on spawning grounds too early, and others can’t find their natal streams.  Their offspring are also far less capable of coping with the stress and adversities, including harvest, pollution, and habitat loss and degradation.

Over-harvest, competition, and straying of hatchery fish has led to the dominance of hatchery fish in the Central Valley salmon populations and homogenization among the populations.  Some populations now survive only in hatcheries or in captive breeding programs.

The Solution

Many of elements of the problem have already occurred and are difficult to overcome.  While some elements are irreversible, it is not too late to limit or reduce some of the negative effects.  A comprehensive set of actions and strategies can avoid, minimize, mitigate, or even reverse these effects.  These actions and strategies should include:

1.      Reduce competition between hatchery and wild salmon in spawning, rearing, and migrating habitat.

  • Do not allow hatchery salmon to spawn in prime wild salmon spawning areas. Sorting at weirs can preclude passing hatchery spawners if hatchery fish are all marked.
  • Do not release hatchery juveniles into rearing and migrating habitats heavily used by remaining stocks of wild salmon. Programs throughout the range of Pacific coast salmon, including the Central Valley, now release hatchery smolts into net pens in rearing areas less frequented by wild salmon.  The best fishery returns to the Central Valley have been from smolts released from coastal net pens.

2.      Reduce straying of hatchery origin spawners into other spawning rivers.

  • Barge hatchery smolts to reduce competition and predation on wild juvenile salmon and decrease the straying of adults that results from trucking.  Barging can help imprint smolts on home rivers and hatcheries.
  • Monitor and sort adult salmon returns in rivers and hatcheries to further eliminate straying.
  • Focus more hatchery production on rivers and streams that do not support significant wild salmon.

3.      Increase harvest of hatchery salmon, while reducing harvest of wild salmon.

  • Focus harvest on hatchery stocks to help protect wild stocks. Release hatchery smolts into locations that focus harvest of adults in areas not frequented by wild salmon.  Adult hatchery salmon tend to stay in or return to areas where smolts were released.
  • Increase existing efforts to reduce the mixed-stock harvesting problem by reducing mixed-stock fishery exploitation rates to levels that are sustainable by wild stocks. Promote selective harvest of hatchery fish by permitting sport fishermen to retain only hatchery fish or to retain more hatchery fish than wild fish.  This would require marking most or all hatchery smolts.

4.      Improve disease control.

  • Hatchery fish experience greater susceptibility to infectious diseases due to higher rearing densities, higher levels of stress and poorer water quality. Diseases/infections can be spread to wild population elements, though research is needed to determine the extent of this threat.
  • Improve filtration systems at hatcheries to reduce the disease threat. This will also alleviate concerns about reintroducing salmon and steelhead upstream of hatcheries.

5.      Improve the genetic makeup of hatchery (and wild) salmon

  • Reverse engineer aspects of genetic diversity that has been selected out. Preferentially spawn 4-5 year-old adults at hatcheries.  Diversify timing of adult runs by breeding hatchery fish throughout the spawning run.  The Mokelumne Fish Hatchery is already implementing many such practices.  “Bad alleles can be purged.”
  • Use conservation hatchery actions to enhance the genetic diversity and fitness to help recover depleted wild populations.
  • Use more wild fish for hatchery broodstocks, particularly fish with more favorable traits.
  • Do not allow adult hatchery fish into spawning habitat used by wild fish.
  • Be more selective in choosing spawners for hatcheries.
  • Develop and support pure strains of wild salmon above dams through trap and haul programs.
  • Promote populations and subpopulations that protect or increase diversity (improve the Portfolio).
  • Develop captive stocks with desired natural traits – with less genetic drift, inbreeding and domestication,
  • Increase monitoring, research, experimentation, and adaptive management on the extent and consequences of domestication selection, as well as steps that may be taken to reduce its effects.
  • Evaluate and operate each hatchery program independently to address its program and its contribution to the overall problem.

Conclusion

Wild salmon populations in California’s Central Valley are already compromised to various degrees by hatchery salmon, over-harvest, and habitat degradation.  More can be done to protect wild salmon production and minimize the threat from hatcheries, while continuing to provide valuable commercial and sport fisheries supported by hatcheries.  We can save our salmon and eat them too.

For a more comprehensive scientific review of these subjects see Sturrock et al. 2019 and Nash et al. 2007.

Predators versus River Flow

I keep emphasizing the need for fall flows to get Central Valley salmon fry, fingerling, sub-yearling smolts, and yearling smolts to and through the Delta to the Bay. This especially applies to wild spring-run and to wild and hatchery winter-run and late-fall run, the Chinook salmon runs most in danger of extinction. Extinction comes from population decline and loss of genetic diversity from lower river flows and fragmented habitat. 1

The reason river flow is important is that flow affects habitat, growth, migration, and predation of emigrating salmon.

The long, slow reservoirs behind the mainstem dams on the Columbia River studied by Conner and Tiffan (2012)2 have habitat similar to the long, slow reaches of the lower Sacramento and San Joaquin rivers in the Central Valley. Furthermore, the Delta with its tides acts as a “main-stem” dam, slowing the outward movement of water through the Delta and salmon exiting to San Francisco Bay. The Delta has also been described as the place “where predators meet prey” – where the effectiveness of predation and the role played by “Anthropogenic Contact Points” is accentuated by modified freshwater flows.

The Sacramento River channel at Walnut Grove is one of the key “anthropogenic” contact points in the Delta. The major outlets from the Sacramento River channel to the central Delta, the Delta Cross Channel and Georgiana Slough, are located here (Figure 1). Lehman et al. (2019)3 describe the predator contact points at this location in Figure 1, including submerged aquatic vegetation, rip-rapped levees, docks, and diversions. The role of these particular contact points in predation on juvenile salmon is no doubt significant.

Lehman et al. point out the difficulty in removing the predators and the problematic contact infrastructure. However, they don’t address the role river flow and associated hydrodynamics play in modifying the effects of predators or specific contact points.

In the fall during the peak of winter-run emigration, Walnut Grove is the place where the Sacramento River channel in the north Delta slows and is “diverted” into the abyss of the central Delta. Few salmon escape the central Delta’s many predators and its “anthropogenic contact points”, including the south Delta export pumping facilities. Under low Sacramento River fall inflows (around 12,000 daily average flow at Freeport), high tides cause most of the water and salmon coming down the Sacramento River to divert into the central Delta via the Delta Cross Channel (DCC) and Georgiana Slough (Figure 2). Those young salmon remaining in the Sacramento channel are then vulnerable to the contact points and predators under lower water velocities. If river inflows are higher and the DCC is closed, the risks to young salmon is greatly reduced (Figure 3).

In conclusion, the Lehman study funded by the Metropolitan Water District describes the role of predators and contact point infrastructure including submerged aquatic vegetation, docks, riprap, and diversions. However, the Lehman study does not address the key factors in the fall loss of juvenile fish in the Delta: lower flows and the diversion of water into the central Delta for export. Closing the Delta Cross Channel and increasing river flows are the prescriptions needed to cut losses of emigrating endangered Central Valley salmon. Cutting south Delta exports in the fall would also be beneficial.

Figure 1. Predation contact points near Walnut Grove in the north Delta. Source: From Lehman et al. 2019.

Figure 2. Measured streamflows at USGS gages near Walnut Grove on 12/1/2019 at 8:00 am high tide. The DCC was open and the Sacramento River at Freeport inflow to the Delta was 12,500 cfs.

Figure 3. Measured streamflows at USGS gages near Walnut Grove on 12/5/2019 at the noon high tide. The DCC was closed and the Freeport inflow to the Delta was 21,000 cfs.

  1. Sturrock et al. 2019. https://onlinelibrary.wiley.com/doi/10.1111/gcb.14896
  2. Connor, W. P., and K. F. Tiffan. 2012. Evidence for parr growth as a factor affecting parr-smolt-survival. Transactions of the American Fisheries Society 141:1207–1218, 2012.
  3. Lehman, B.M., et al. 2019. https://escholarship.org/uc/item/2dg499z4

Dutch Slough Tidal Marsh Restoration

The Dutch Slough Tidal Restoration Project,1 newly redesigned (Figure 1), has some improved design elements, but remains flawed and potentially detrimental to Delta native fishes. Unless the flaws are overcome, the project will be a huge waste of limited Delta restoration funds.

First, the proposed project’s location within the Delta (Figure 2) is extremely detrimental.

  1. The location is an eastward extension of Big Break, an open water of the west Delta that is infested with non-native invasive aquatic plants and that breeds non-native fishes.
  2. The project is located on Dutch Slough, detrimentally warm in summer (Figure 3), with net flows that are negative and eastward toward the south Delta export pumps (Figure 4).

Second, and equally important, the project as designed would further contribute to the existing detrimental non-native vegetation and warm water problems.

  1. The extensive new dead-end slough complexes will become infested with invasive plants and will contribute to lowering turbidity and warming.
  2. The new subtidal habitat will further add to that in Big Break with more invasive plants and breeding and rearing habitat for non-native fish.

Third, the new habitat will attract breeding smelt and rearing juvenile salmon into an area where their eventual survival is highly questionable.

Can design changes overcome these flaws? Yes, but only in combination with other regional fixes.

  1. Big Break must first be restored along the lines being considered and studied in the Franks Tract Restoration Feasibility Study.
  2. A tide gate must be installed on east Dutch Slough, similar to that being considered for False River in the Franks Tract restoration. (This would fix the negative net flows toward south Delta exports and reduce salinity intrusion.)
  3. Open-water subtidal habitat should be eliminated. (Make the subtidal element diked-off non-tidal marsh.)
  4. Dead-end sloughs should allow flow-through to increase tidal circulation.
  5. Finally, more freshwater outflow should be allocated by reducing south Delta exports in low outflow conditions, in order to reduce salinity intrusion.

Figure 1. Conceptual design of Dutch Slough restoration project.

Figure 2. Location of Dutch Slough Project in the Delta.

Figure 3. Water temperature in Dutch Slough in 2014 and 2015.

Figure 4. Daily net flows in Dutch Slough 2007-2018.