Little Action on 2014 Salmon Recovery Plan

The 2014 Recovery Plan for Central Valley salmon and steelhead includes actions designed to lead toward recovery of listed Central Valley winter and spring run salmon salmon and steelhead.  After ten years, there has been little progress and improvement, and populations are at or near record lows.  The problem is not the plan.  It is lack of implementation and progress toward implementation.  Yet despite lack of progress, various agencies are advancing new major water projects, the extension of water right permits, and the update of water quality control plans that would further threaten the state’s fishery resources if Recovery Plan actions are not implemented.

What are the key actions in the Recovery Plan whose lack of progress hinders recovery?1

  • Develop and implement an ecosystem based management approach that integrates harvest, hatchery, habitat, and water management, in consideration of ocean conditions and climate change. Such a plan, strategy, or approach does not exist.  While a comprehensive coordinated operations program exists for water supply, none exists for fisheries and aquatic resources.
  • Implement the recommendations and guidelines of the California Hatchery Scientific Review Group (http://cahatcheryreview.com/). Many recommendations and guidelines have yet to be implemented.2
  • Implement and evaluate actions to minimize the adverse effects of exotic (non-native invasive) species (plants and animals) on the aquatic ecosystems used by anadromous salmonids. No progress.  Predator effects remain high from lack of adequate river flows and poor hatchery release practices.
  • Incorporate ecosystem restoration including breaching and setting back levees into Central Valley flood control plans (i.e., FloodSafe Strategic Plan and the Central Valley Flood Protection Plan). Central Valley floodplains present great opportunities as salmonid habitat. However, most of them today remain one-way detours without escape, and thus a threat to salmon.
  • Improve the timing and extent of freshwater flow to the San Francisco Bay region to the benefit of juvenile and adult salmonids by modifying water operations in the Central Valley to support flows that mimic the natural hydrograph. Water flows remain compromised and are allowed to degrade even further in droughts.
  • Develop, implement, and enforce new Delta flow objectives that mimic historic natural flow characteristics, including increased freshwater flows (from both the Sacramento and San Joaquin rivers) into and through the Delta and more natural seasonal and interannual variability. No progress, bitterly contested.
  • Reduce hydrodynamic and biological impacts of exporting water through Jones and Banks pumping plants. Record exports and pelagic habitat degradation continue.
  • Provide pulse flows of approximately 17,000 cfs or higher as measured at Freeport periodically during the winter-run emigration season (i.e., December-April) to facilitate outmigration past Chipps Island. There are no late fall pulse protections or prescribed reservoir releases during the key periods that winter-run salmon emigrate through the Bay-Delta.3
  • Restore, improve and maintain salmonid rearing and migratory habitats in the Delta and Yolo Bypass to improve juvenile salmonid survival and promote population diversity. Lots of talk and little action over the past decade.
  • Minimize the frequency, magnitude, and duration of reverse flows in Old and Middle River to reduce the likelihood that fish will be diverted from the San Joaquin or Sacramento rivers into the southern or central Delta. Limited restriction in export-induced reverse flows with limited benefit; plans to allow higher levels of exports.
  • Continue to evaluate head of Old River barrier operations to identify and then implement the best alternative for maximizing survival of juvenile steelhead and spring-run Chinook salmon emigrating from the San Joaquin River. Evaluation continues with no implementation.
  • Modify Delta Cross Channel gate operations and evaluate methods to control access to Georgiana Slough and other migration routes into the Interior Delta to reduce diversion of listed juvenile fish from the Sacramento River and the San Joaquin River into the southern or central Delta. No progress.  Gates remain open in winter-run emigration season (Nov-Dec).  No resolution of Georgiana Slough problem.
  • Through additional releases in the San Joaquin River system, augment flows in the southern Delta and curtail exports during critical migration periods (April-May), consistent with a ratio or similar approach. Continuing conflict and lack of resolution.
  • Design and implement a project(s) to: (1) allow adult salmonids (and sturgeon) from the Sacramento Deep Water Ship Channel (SDWSC) to pass the channel gates and enter the Sacramento River (or block adult salmonids from entering the SDWSC); and (2) minimize fish passage from the Sacramento River into the SDWSC. No progress.
  • Establish Vernalis flow criteria that incorporate the flow schedules of the San Joaquin River and tributaries in order to increase juvenile salmonid outmigration survival. Continuing conflict and lack of resolution.
  • Evaluate whether predator control actions (e.g., fishery management or directed removal programs) can be effective at minimizing predation on juvenile salmon and steelhead in the Delta. Continuing evaluation and minimal resolution.
  • Develop and implement a program to reintroduce winter-run Chinook salmon, spring-run Chinook salmon, and steelhead to historic habitats upstream of Shasta Dam. The program should include feasibility studies, habitat evaluations, fish passage design studies, and a pilot reintroduction phase prior to implementation of the long-term reintroduction program. Minimal progress and no implementation.
  • Restore and maintain riparian and floodplain ecosystems along both banks of the Sacramento River to provide a diversity of habitat types including riparian forest, gravel bars and bare cut banks, shady vegetated banks, side channels, and sheltered wetlands, such as sloughs and oxbow lakes following the guidance of the Sacramento River Conservation Area Handbook (Resources Agency of the State of California 2003). Minimal progress and lack of funding and interest.
  • Develop and implement a river flow management plan for the Sacramento River downstream of Shasta and Keswick dams that considers the effects of climate change and balances beneficial uses with the flow and water temperature needs of winter-run Chinook salmon, spring-run Chinook salmon, and steelhead. The flow management plan should consider the importance of instream flows as well as the need for floodplain inundation.  No progress, further degradation.
  • Avoid full power peaking at Trinity and Carr Power plants during sensitive periods for water temperatures to reduce water temperatures in the Sacramento River. Evaluate impacts of power peaking operations in the Trinity River, Sacramento River and Clear Creek.  No progress and lack of action.
  • Providing and/or improving fish passage through the Yolo Bypass and Sutter Bypass allowing for improved adult salmonid re-entry into the Sacramento River (long-term). Limited progress and lack of implementation.
  • Implement studies designed to quantify the amount of predation on winter-run Chinook salmon, spring-run Chinook salmon, and steelhead by non-native species in the Sacramento River. If the studies identify predator species and/or locations contributing to low salmonid survival, then evaluate whether predator control actions (e.g., fishery management or directed removal programs) can be effective at minimizing predation on juvenile salmon and steelhead in the Sacramento River; continue implementation if effective.  No progress.

In conclusion, the extension of water rights permits and the update of water quality control plans offer opportunities to incorporate all of the above and other Recovery Plan actions that would lead toward Central Valley salmon and steelhead recovery.  These processes should not proceed or be approved without comprehensive acknowledgement and incorporation of recovery actions.

Winter Pulsed Flows for Fall Run Salmon

There has been a series of storms in the Central Valley in early winter 2019 that have stimulated the migration of salmon fry and smolts in the lower Sacramento River toward the Bay-Delta (Figure 1). However, these storms have not created flow pulses in the 25 miles of prime spawning habitat in the Sacramento River directly downstream of Keswick Dam (River Mile 300) (Figures 2 and 3). High flows at Bend Bridge (RM 250) have originated from largely un-dammed Cow, Cottonwood, and Battle creeks. Although inflow to Shasta and Keswick reservoirs has exceeded 50,000 cfs during two recent storm events (Figure 4), these reservoirs are releasing only a few thousand cfs.

Based on the Red Bluff screw trap catch (top chart in Figure 1), there are likely many wild fry in the upper river directly downstream of Keswick Dam that could take advantage of flow pulses to start their 300–mile journey toward the San Francisco Bay-Delta and its optimal fry rearing habitat. Flow pulses of 3000-5000 cfs during storm events added to the existing Keswick release could go a long way toward increasing the production of wild fall-run Chinook salmon.

Figure 1. Screw trap collections of fry fall-run salmon at Red Bluff (RM 240) and Tisdale Weir (RM 120) August 2018 to mid-January 2019.

Figure 2. Sacramento River flow at Keswick Dam (RM 300) (red line) and Bend Bridge (RM 250) (green line) 10/1/18-1/16/19.

Figure 3. Map of upper 100 miles of Sacramento River downstream of Keswick Dam with approximate percent of salmon spawning by sub-reach. (CDFW data)

Figure 4. Inflow to Shasta Reservoir in January 2019.

Suisun Bay Zooplankton in Droughts

Suisun Bay zooplankton are important prey for Bay-Delta fish populations, including smelt and juvenile salmon.  During the recent 2012-2016 drought, the State Water Board issued temporary urgent change orders (TUCOs) that allowed lower Delta outflow than would normally be required in Critically Dry water years.  Specifically, those Board orders allowed lower outflow in spring of 2014 and 2015. To evaluate the effects of these orders, I looked at June outflow versus June density of cladoceran and calanoid copepods, the primary fish prey in Suisun Bay and Marsh, the prime east Bay nursery area.

Zooplankton sampling stations in area of Suisun Bay and Suisun Marsh. I used June survey densities for stations 28, 32, 48, 54, and 60 to represent food available to young salmon and smelt.

Cladocerans

Cladocerans, sometimes called “water fleas,” are generally most prevalent in freshwater portions of the estuary, and would be expected to have lower density as brackish water encroaches in Suisun Bay with lower outflow. Cladoceran density was near zero in June 2014 and 2015, when outflow fell below 5000 cfs under the TUCOs (Figures 1 and 2) and EC reached an unprecedented 13-16 millimhos in June at Mallard Island in Suisun Bay (CDEC data). Cladoceran densities were highly variable in the outflow range of 6000-8000 cfs.

Calanoid Copepods

Calanoid copepods are another important prey of juvenile fish in Suisun Bay/Marsh. They reside in fresh and brackish waters of the Bay-Delta estuary. Calanoid copepod adult density was near zero in June 2014 and 2015, when outflow fell below 5000 cfs under the TUCOs (Figures 3 and 4) and EC reached an unprecedented 13-16 millimhos in June at Mallard Island in Suisun Bay (CDEC data). Calanoid copepod adult densities were highly variable in the outflow range of 6000-8000 cfs.

Conclusion

Maintaining Delta outflow in spring at least as great as is required by existing water quality standards is important in maintaining the productivity of zooplankton in Suisun Bay and Suisun Marsh. June outflows greater than existing requirements generally increased the productivity of these important prey for fish.

Figure 1. Density/m3 (log transformed) of total cladocerans in Suisun Bay/Marsh in June surveys 2000-2017. Note very low densities during 2012-2016 drought, especially in 2014 and 2015 when TUCOs allowed outflow to fall below 5000 cfs.

Figure 2. Density/m3 (log transformed) of total cladocerans in Suisun Bay/Marsh in June surveys 2000-2017 versus average daily June Delta outflow for the year. Note the high variability in density in the outflow range of 6000-8000 cfs. The two dots on the x axis represent 2014 and 2015.

Figure 3. Density/m3 of calanoid copepod adults in Suisun Bay/Marsh in June surveys 2000-2017.
Note very low densities during the 2013-2015 drought, especially in 2014 and 2015 when TUCOs allowed outflow to fall below 5000 cfs.

Figure 4. Density/m3 of calanoid copepod adults in Suisun Bay/Marsh in June surveys 2000-2017 versus average daily June Delta outflow for the year. Note the high variability in density in the outflow range of 6000-8000 cfs. The two dots just above the x axis represent 2014 and 2015.