Sustaining wild Salmon and Steelhead above Central Valley dams

The Case for Two-Way Trap and Haul

Why should we expand spawning populations of listed salmon and steelhead to areas above dams and impassible falls in the Central Valley? The answer is: because the genetic makeup and wild traits of populations upstream of existing barriers can be controlled, restored, and preserved.

At present, the genetic makeup of salmon and steelhead populations below dams is continually being compromised by hatchery fish and strays to and from other watersheds. The one population of winter-run Chinook is confined to the spawning reach immediately below Keswick Dam and thus is subject to the potentially drastic whims of nature and man. That population is further being compromised by the increasing threat of hatchery degradation of the gene pool as winter-run hatchery fish further dominate the adult spawning population. Small, self-sustaining populations of spring-run Chinook and steelhead remain in only a few watersheds. They too are continually being threatened by strays and hatchery fish.1

One solution to maintaining genetic integrity by limiting genetic influence from hatchery-produced fish and interbreeding of genetically or behaviorally distinct runs is to implement trap-and-haul programs in isolated reaches above dams.

The National Marine Fisheries Service included requirements to establish winter-run Chinook trap-and-haul populations above Shasta Reservoir in 2009, 2010, and 2014 biological opinions on Central Valley Project (CVP) and State Water Project (SWP) operations. CALFED proposed introducing spring-run Chinook above Yuba River dams. Extensive studies have been conducted on reintroducing salmon in these areas. The requirement to establish populations upstream of Shasta has been dropped in the Trump administration’s October 2019 biological opinion for the CVP and SWP. For the moment at least, the requirement remains in state of California plans.2

The California Department of Fish and Wildlife’s California Endangered Species Act Take Permits for CVP and SWP operations should require reintroduction of salmon and steelhead upstream of an array of dams in the Sacramento River watershed. All of the sites I recommend are affected by the CVP and SWP. The state should also consider locations in the San Joaquin and Klamath River watersheds. The Klamath watershed is also affected by Reclamation’s Klamath Project, and is the present subject of the country’s largest dam removal project.

In considering potential sites I focused on the ability to maintain experimental controlled conditions as well as optimum habitat quality sites. In most cases, that meant minimal flow variation and high quality, cold reaches dominated by spring water. The sites need not be in the historical range, but should be in historically occupied watersheds (e.g., they could be upstream of impassible falls in watersheds that historically held salmon and steelhead.).

I suggest five sites in the Sacramento River watershed (Figure 1).

  1. Upper Sacramento River (above Lake Shasta) – below Lake Siskiyou dam upstream of Dunsmuir in the Box Canyon/Shasta Springs reach.
  2. Upper McCloud River (above Upper McCloud Falls) – spring-fed reach above Larkin Dam on south flank of Mt Shasta.
  3. Upper Battle Creek – Ripley Creek, tributary of South Fork, spring-fed, although presently its flow is diverted by PG&E to South Fork Powerhouse.
  4. Upper North Fork of Feather River – above or below Lake Almanor.
  5. Upper North Yuba River – above Bullards Bar Reservoir.

I have studied all of these sites and consider them feasible for reintroduction. Most have been considered for reintroduction by state and federal resource agencies. Reintroduction strategies may include releases of native-strain adult spawners, planting of eyed eggs, fry, or fingerlings, then capture and trucking to locations downstream of dams.

For more on reintroducing salmon above dams see:
https://podcast.barbless.co/reintroduction-of-winter-run-chinook-into-the-mccloud-river-jon-ambrose-noaa-nmfs/

https://www.webpages.uidaho.edu/UIFERL/pdf%20reports/Keefer%20et%20al.%20%202010%20WIL%20Chinook%20prespawn%20mortality%201.pdf

https://fishwithjd.com/2015/05/07/new-plan-developing-to-get-spring-chinook-into-north-yuba-upstream-of-bullards-bar-reservoir/

Figure 1. Historical range and present range of salmon in Sacramento-San Joaquin watershed, with suggested five locations for reintroduction via two-way-trap-and-haul shown as red dots.

The Good, the Bad, and the Ugly in the New Non-Jeopardy Biological Opinions for CVP/SWP

The Endangered Species Act (ESA) directs all federal agencies to work to conserve endangered and threatened species and to use their authorities to further the purposes of the Act. The purpose of the Act is to protect and recover imperiled species and the ecosystems upon which they depend. Protect means to not allow “take” of listed species. If some take occurs despite best efforts, then “reasonable and prudent” alternatives (RPAs) may be needed to protect the threatened or endangered species.

The US Bureau of Reclamation and its partner the California Department of Water Resources (permittees) operate the federal Central Valley Project (CVP) and the State Water Project (SWP) under federal and state ESA “take” permits issued in 2008-2009 biological opinions that included RPAs. The RPAs constrained water supply deliveries and other project operations during the past decade to protect listed salmon, smelt, sturgeon, and steelhead.

Over the past decade, the parties have reinitiated consultation to revise take permits and RPAs. The initial motivation for reinitiation was that RPAs and take limits were not protecting or recovering the listed species. The US Fish and Wildlife Service (USFWS) and the National Marine Fisheries Service (NMFS) recognized that more stringent measures were needed. A series of draft opinions were developed with further protections, culminating with a July 1, 2019 draft jeopardy opinion from NMFS on Reclamation’s proposed action as of that time. A jeopardy opinion occurs when an action is reasonably expected, directly or indirectly, to diminish a species’ numbers, reproduction, or distribution so that the likelihood of survival and recovery in the wild is appreciably reduced.

Reclamation updated its “proposed action” in response to the draft jeopardy opinion. “It must also be acknowledged that the current status of all these species continues to be imperiled, and that one of the objectives of the proposed action is to maximize the available supply of water for irrigation, municipal, and industrial deliveries.”1 Reclamation doubled down. Reclamation’s most recent proposed action includes some provisions of the 2008/2009 biological opinions’ RPAs and recent jeopardy draft BO. In response, the Services relented under pressure from the Trump administration, replaced technical staff with a new group of managers, and recently issued final non-jeopardy opinions.

The new proposed action from Reclamation can now go into effect without RPAs that would hinder Reclamation from maximizing water deliveries. The new Biological Opinions will govern project operations under a wide array of vague commitments to protect and recover listed species: some good, some bad, and some simply ugly.2

The Good (Well, as Good as it Gets)

  1. Delta Smelt Conservation Hatchery
    This is long past due. However, the proposal is vague and limited in potential scope and funding commitment.
  2. New Habitat
    Most measures that require new habitat in the new BO were prescribed in past BOs. Now there are new vague commitments. Some listed species (e.g., Delta smelt) have populations too small to benefit from new habitat.
  3. Hatchery Management
    New and updated old prescriptions, though vague, are badly needed, especially for converting the program focus from mitigation hatcheries to conservation hatcheries.
  4. Proposed Funding for research and restoration
    The BOs contain an estimated total of $1.5 billion dollars in proposed funding to support threatened and endangered fish survival and recovery through research and restoration actions. However, the proposed funding is not dedicated and is vague, particularly in that much of the effort and funding may go to prior commitments that have not been funded.
  5. Delta Cross Channel Improvements
    Proposed upgrades to the Delta Cross Channel Gates are helpful but vague. The Delta Cross Channel should be screened, as should nearby Georgiana Slough.
  6. Modifying the Head of Old River Scour Hole
    This action is OK but addresses only one of many predation hotspots for salmon and steelhead caused by human actions and man-made structures in lower San Joaquin River.
  7. Fish Passage on Deer Creek (a non-Project watershed)
    This is one positive action for listed spring-run salmon among many in NMFS’s Central Valley Salmon Recovery Plan. All of the actions in the Recovery Plan should be included and funded. Deer Creek, a tributary to the lower Sacramento River, has a spawning run of wild spring-run salmon. Deer Creek does not have a project dam on it, but Deer Creek salmon pass through the lower Sacramento River and Delta. Deer Creek salmon and all other salmon-bearing tributary populations are thus affected by project operations.
  8. Adult Straying Barrier on the Knights Landing Outfall Gate (a flood and drainage system)
    This was constructed under prior commitments but failed.
  9. A “drought toolbox” to prioritize a proactive approach to drought planning, including early coordination with senior water right users
    Proactive coordination is fine and good, but the BOs contain no commitment to reduce diversions by senior Settlement and Exchange contractors or any others during droughts.
  10. Support for NMFS Steelhead Monitoring and Collaboration Activities with Non- Project Tributaries
    Monitoring may inform mitigation. However, monitoring in itself is not mitigation. All recovery plan actions should be supported because CVP/SWP operations and facilities have had major adverse effects on all Central Valley steelhead populations.
  11. $14 million commitment to expedited implementation of the Battle Creek Restoration Project including reintroduction of winter-run Chinook salmon
    The commitment to fund actions on Battle Creek is long overdue, but the funding in the BO is inadequate by an order of magnitude.
  12. A stronger commitment to actions maintaining low-salinity habitat in the Delta Smelt Summer-Fall Habitat Action with commitments regarding Suisun Marsh Salinity Control Gate (SMSCG) operations and projects for other elements of habitat
    It is important to acknowledge the importance of summer-fall habitat representing half of the smelt life-cycle, but the commitment in the BO is vague and likely ineffective as formulated. Rather than being used more often, the SMSCG should simply be removed. It has been a detriment to smelt, salmon, steelhead, and sturgeon populations since its use began in 1989.

The BAD

  1. Drought Mitigation
    Drought mitigation in the BOs focuses on maintaining Shasta Reservoir’s cold-water-pool. The proposed action drops mitigation actions for wet years such as Fall X2. The proposed action drops previous OMR constraints that provided some protection in drought years. The one-hand-giveth-while-the-other-taketh-away approach is an old tired gambit. The ostensible improvement at Lake Shasta eliminates numeric targets for Shasta carryover storage.
  2. Real time management – protect when and where the fish are
    This is poor prescription because some listed species populations are so low that they are undetectable (e.g., Delta smelt). Larval life stages also go undetected. Past detection rates even for larger populations have been poor, and actions to reduce impacts have been gamed and trimmed to the bone. Real time detection does not protect primary productivity and food sources and other elements of critical habitats. The managers charged with managing have a long history of choosing water supply over fish protection.
  3. A more detailed description of Shasta Dam operations and a commitment to Cold Water Management Tiers
    This prescription does not protect listed winter-run salmon in droughts from thermal shock or dewatering of redds, which are the primary factors in recent low survival and production. Prior RPA and Recovery Plan requirements to fix problems with Spring Creek powerhouse (Whiskeytown Lake thermal curtain) and Shasta Dam warm water power releases are not included in the new salmon BO.
  4. “New” Science
    A commitment to maintaining long-term monitoring programs and recognizing past and present science is needed. “New” science funded and conducted by water contractors or federal/state project operators will ensure any new science will be biased – foxes assessing their effects on the henhouse. The science and its presentation and analyses have become more and more controlled by water supply entities, and less and less by resource agencies. The BOs give more control of science to water suppliers. The revisions to the draft BOs are clear evidence of the new realignment of roles and new controls on science.
  5. Performance Metrics for managing Old and Middle River reverse flows to limit salmonid loss to similar levels observed under the previous BiOp through explicit reductions in export pumping.
    The BOs’ performance measures for reverse flows are vague, ineffective, and unenforceable. Wild components of salmon populations were hard hit in droughts under previous BOs. “Similar” levels of loss are not protective and will not promote recovery.
  6. Performance Metrics for incubation and juvenile production of salmonids under the proposed Shasta Cold Water Pool Management strategy
    The BOs’ performance measures for cold water management at Lake Shasta are vague, ineffective, and unenforceable.
  7. Commitments to manage Old and Middle River reverse flows for limiting larval and juvenile delta smelt entrainment based on modeled recruitment estimates
    OMR rules have been one of the major restrictions on exports under the past BOs. The rules proved beneficial to the listed species survival (primarily reduced salvage and improved through-Delta survival of tagged salmon smolts). The new strategy would allow changes that would allow greater levels of exports under OMR reverse flow prescriptions. The poor survival of San Joaquin salmon under existing rules would remain poor or further decrease. Entrainment of young smelt (not measured under existing rules), an existing serious concern, would only worsen. Modeling entrainment risk has not worked and has not been verifiable. The main risks to smelt are pulling larvae into the central Delta with its poor habitat (not just to the south Delta pumps) and the destruction of their critical pelagic rearing habitat.
  8. Independent Review Panels to evaluate the science behind actions and outcomes
    This is nothing new. There have been so many “independent” review panels. I remember working with Pete Chadwick back in the mid-70s. He consulted on my projects on the Hudson River Estuary. He and his CDFG staff working on the Bay-Delta were on the cutting edge of estuary science. They trained the next generation and they in turn trained the next. Outsiders have only verified what CDFG already well understood. Same goes for NMFS and the USFWS, as well as UC Davis. Together as IEP they manage Bay-Delta and Central Valley science more than adequately with the help of a huge cadre of capable scientists among NGOs. Water agencies and other water suppliers just can’t handle the truth, so they hire their own consultants and many outside “independent” consultants.
  9. Ramping rates specificity for reservoir releases to reduce the risk of stranding
    Ramping rates do not work for eggs and fry salmon that are in gravel beds for up to several months. Reductions in flows from Keswick Reservoir after winter-run fry have left their nests (redds) in the fall strands up to 80% of new fall-run redds.

The Ugly

  1. Commitment to implement appropriate actions after two years of low winter-run Chinook salmon egg-to- fry survival.
    Shasta operations in the 2014 and 2015 drought killed 90-95% of the egg production of winter-run salmon. The new Salmon BO would make that acceptable under the ESA. It would stretch the no-take standard to no take in more than two years out of three.
  2. More specificity on collaborative planning with specific habitat restoration and facility commitments.
    More planning for habitat restoration and facilities is not needed. Reclamation, DWR and other responsible agencies should get on with prior commitments. The history of foot-dragging on habitat restoration in the Central Valley is a worthy rival to the foot-dragging by PG&E in maintaining and upgrading its infrastructure.
  3. A commitment to sediment supplementation and food-web studies for the protection of delta smelt.
    As proposed the supplementation of sediment would come in the form of the discharge of warm, polluted agricultural drainage water full of non-native predatory fish into critical habitats of listed fish.
  4. Dynamic, real-time monitoring of changing conditions and potential species impacts, within an improved scientific and adaptive-management-based decision-making framework; avoiding or minimizing fishery impacts while increasing operational flexibility.
    Real time management will not work for rarer listed species like Delta smelt. This has been tried for three decades and has not worked. The adaptive managers will be the same managers who produced the revised non-jeopardy BOs. “Operational flexibility” is a buzzword for increased diversions, primarily Delta exports.
  5. Operational rules that lay the foundation for eventual voluntary agreements on water flows for rivers that feed into the delta. Those agreements promise even greater protections and investments in fish and the environment.
    Most of the “even greater protections” will have to backfill the protections that these BOs took away. The Voluntary Agreements offer pennies on the dollar in terms of necessary flow through the Delta into the San Francisco Bay.
  6. Eliminating or Modifying Existing RPAs and Take Limits
    • Modifying year-round temperature and Shasta reservoir storage management program to minimize effects to endangered winter-run salmon.
      NMFS and CDFW were just starting to get it right. NMFS’s 2017 draft RPA for Shasta would have required stronger carryover storage requirements.
    • Long-term passage prescriptions at Shasta Dam and re-introduction of winter-run to its native habitat in the McCloud and/or Upper Sacramento Rivers.
      They were ready to start this program after promising initial feasibility studies. The foot draggers strung it out until Trump administration officials threatened in 2019 to arrest DWR personnel who were installing equipment to begin a pilot implementation.
    • Old and Middle River flow levels that limit the strength of the reverse flows
      There will be less of the needed restrictions under Reclamation’s new plan.
    • Prescriptions for additional technological measures at the facilities to enhance screening and increase survival of fish.
      There will be fewer planned upgrades to project facilities to protect fish than were promised under the previous BOs.
    • Prescribed additional measures to improve survival of San Joaquin steelhead smolts, including both increased San Joaquin River flows and export curtailments.
      No longer apply.
    • Prescribed flow management standard, a temperature management plan, additional technological fixes to temperature control structures, and, in the long term, a passage at Nimbus and Folsom dam to restore steelhead to native habitat.
      No longer apply.
    • Prescribed year-round minimum flow regime necessary to minimize project effects to each life-stage of steelhead, including new springtime flows that will support rearing habitat formation and inundation, and create pulses that allow salmon to migrate out successfully.
      No longer apply.
    • The Fall X2 provision has been eliminated.
      This flow-salinity RPA protected longfin and Delta smelt in summer and fall of wet years.
    • Take limits have been eliminated.
      They should have been revised to be more protective.

What is Missing

So much is missing that is within state and federal governments’ power and authority in the final approved Reclamation proposal. Here is a limited selection.

  • Effective Management of Shasta Cold-Water Pool
    Missing from the BOs are controls of Spring Creek powerhouse warm water releases into Keswick Reservoir, modifications to hydropower operations, long term Shasta storage rules, and modifications of water contractor deliveries. Combinations of these actions would have alleviated winter run salmon recruitment failures in 2014 and 2015. Reclamation’s approved proposal would allow such drastic recruitment failures in future droughts.
  • Commitment to comply with water quality standards on flow, water temperature, salinity, and export restrictions
    Reclamation has made no commitment to comply with state water quality standards or other state laws.
  • Commitment to provide needed pulsed flows
    Coordinated pulsed flows are needed to increase survival of hatchery and wild salmon. None are included in Reclamation’s plan, with the possible exception of a pulse from Shasta when it is likely to spill anyway.
  • Commitment to implement recovery plan actions
    Recovery, not just protection, is needed and is required by the ESA. These BO’s do not address recovery plans. The ESA goes beyond simple mitigation. The ESA focuses on minimization of effects, enhancement, and recovery.

In Conclusion: Ugly

Reclamation’s proposed action has been approved by the Services. The proposed action includes some good concepts for protective measures (though generally the requirements are vague, underfunded and not enforceable), and a suite of bad and downright ugly actions that will harm affected listed fish species. The overall mix will lead to much confusion, wringing of hands, blaming, ignoring of responsibility, initial lawsuits, and (if the initial lawsuits fail) further lawsuits when fish metrics fail to show improvement. Some actions will take time to implement, while some are already too little too late.

The Services should have issued jeopardy opinions with a suite of appropriate RPAs. That did not happen. Instead, the Services are allowing further risk of extinction to the listed species. The best example of this is allowing expected temperature-dependent egg mortality levels for Sacramento River winter-run Chinook salmon to occur in “Tier 3 and 4 years.” Mortality due to allowed temperature exceedance was a major cause in the recent decline in the winter-run salmon population, one of the few species listed as “endangered” rather than the more common “threatened” designation. The effect the salmon BO will allow is entirely avoidable and within the control of the state and federal agencies involved in permitting the CVP. NMFS has designated winter-run as a “Species in the Spotlight”; it’s more likely that it is now a “Target for Extinction.”

  1. USFWS summary, p. 13.
  2. The US Fish and Wildlife Service’s summary of both its own Biological Opinion for smelt and the National Marine Fisheries Service’s Biological Opinion for salmon, steelhead and green sturgeon is available at: https://www.fws.gov/sfbaydelta/cvp-swp/documents/ROC_on_LTO_Summary_FINAL.pdf
    For the complete USFWS and NMFS Biological Opinions and appendices, go to: https://www.fws.gov/sfbaydelta/CVP-SWP/index.htm

Analyzing Fish Population Dynamics in the Bay-Delta

I have been analyzing the declines in Bay-Delta and Central Valley fish populations for over 40 years. Fish population dynamics were the focus of my college education and my 50-year career in environmental impact assessment. I have participated in all the major efforts to understand the Bay-Delta fish population declines. From all of these efforts, it is clear to me what has caused the major fish population crashes.

Pre-1970

First and foremost are the well known historic factors, the original sins pre-1970s of diverting water, building levees and dams, urban development, gold mining, cutting forests, polluting rivers, over-fishing, and introducing non-native species. These explain many of the major native fish population declines and extinctions such as the Sacramento perch and San Joaquin spring-run Chinook salmon, and the near extinctions of Delta smelt, green sturgeon, winter-run and spring-run salmon, and steelhead.

Post-1970

Since 1970, there have been dramatic declines in salmon, steelhead, smelt, sturgeon, splittail, and striped bass, often described as “recruitment failure” or failure to reproduce. While some of the blame most certainly is on continuing effects of the aforementioned original sins, the major post-1970 shifts were the consequence of a new array of stresses that hit the whole fish community, especially native fish populations. Most certainly the droughts of 76-77, 87-92, 01-02, 07-09, and 12-15 were a major underlying factor; however, it was the man-made responses to the droughts that caused most of the damage. Asian clam and other non-native aquatic invertebrate invasions to the Bay-Delta in the 80s were another stress, in part brought on by the aforementioned factors. Poor water management response to these new threats has caused further damage. The big culprits of change were the water management stresses described below.

1. State Water Project

The addition of the State Water Project (SWP) in the mid-1970s nearly tripled Delta export capacity (4400 to 11,400 cfs pumping rate1) and annual exports (2 million acre-feet to 6 million acre-feet annual exports). The additional Delta exports had huge fish population effects in the mid-70s from salvage mortality and entrainment of young fishes, as well as on fish habitat conditions in the rivers, Delta, and Bay. These stresses resulted in major population declines, which in turn resulted in the imposition of export restrictions in new water quality standards in 1978 (D-1485), and eventually to species listings under the Endangered Species Act in the 1990s.

2. Reservoir Operations

The increase in exports changed reservoir operations, including within-year reservoir release strategies and long-term multiyear reservoir storage patterns. Reservoir storage was depleted faster in droughts because of higher water supply demands. These effects continue today.

3. Water Supply Demands

Ever-increasing water supply demands from agricultural and municipal users have reduced river flows, Delta outflow, and reservoir storage. It’s not only the Delta’s 6 million acre-feet of exports, but the more than 20 million acre-feet from other Central Valley water diversions.

4. Invasive Species

Invasions of non-native clams, shrimp, fish, and zooplankton species since the 1970s have occurred in-part due to changes in Bay-Delta hydrology and water quality, as well as physical and biological habitat conditions. Delta pelagic (open water) habitat is now dominated by low-productivity reservoir water. The low salinity or mixing zone of the estuary became far less productive because of species invasions and reservoir water moving through to the south Delta export facilities, taking productive low-salinity habitat with it. The Delta is warmer from higher warm river inflows from spring through fall to feed water project exports, further favoring non-native warm-water fishes. Turbidity is lower, favoring non-natives. Invasive aquatic vegetation benefits from low turbidity, and the vegetation further favors non-native fishes over native fishes.

Post-1990

Since 1990, there have been steps backward that have undermined effective strategies and actions that had been undertaken beginning in the late 1970s to help depressed fish populations. Below are five examples in a long list of actions/changes.

1. Changes to D-1485

Beginning In 1978, Delta water quality standards in Decision 1485 placed restrictions on Delta exports, improved Delta outflows, and set salinity standards that had benefits for native fishes. Beginning in the 1990s, these post-1970 constraints on water diversions were changed, ignored, or eliminated. For example, new standards in D-1641 (1995 Accord) dropped the D-1485 June-July export restrictions.

2. Eliminating VAMP Export Restrictions and Higher Outflow Requirements in April and May

The Vernalis Adaptive Management Plan (VAMP) from 2000-2009, and its operational precursors under the CVPIA (1991) and the 1995 Accord, sought to protect Central Valley salmon and Delta native fishes by reducing April-May Delta exports and increasing spring Delta inflows and outflows. During the VAMP years, exports were restricted to less than 2000 cfs in April-May to protect fish (Figure 1). In the post-VAMP decade, restrictions were lifted and exports increased, especially in post-drought recovery wet years 2011 and 2017 (Figure 2).

3. Temporary Urgency Change Petitions (TUCPs) and Orders

Temporary urgency change orders during the recent drought allowed April-May Delta outflow to fall to around 5000 cfs in 2014 and 2015, from the normal near-10,000 cfs lower limit (Figure 3). Such low outflows in combination with Delta exports are devastating to Delta native fishes and Central Valley salmon and steelhead.

4. Delta Channel Barriers

The operation of the Delta Cross Channel, Head of Old River, South Delta, and False River barriers helps to keep export salinity down by funneling the fresher Sacramento River water to the south Delta export pumps. This increases the efficiency of exports in taking reservoir water in drier years and seasons. With the exception of the Head of Old River, barrier operation also funnels Delta native fish production (pelagic eggs and juveniles) and migrating young salmon (and their low salinity habitat and food sources) directly to the export pumps instead of to the Bay.

5. Suisun Marsh Salinity Control Gates

Since the installation of the Suisun Marsh Salinity Control Gates (SMSCG) in Montezuma Slough in 1989, the Slough and Marsh no longer function as critical low salinity habitat in drier years and seasons. Without high freshwater inflow, the Slough and Marsh no longer maintain the high biological production the once contributed to the Bay. The following excerpt from a DWR 2019 blog post inadvertently describes how limited the benefits of Suisun Marsh have become in the absence of flow:

DWR launched a pilot project last year that directed more fresh water flow into Suisun Marsh. The action involved opening salinity control gates in the summer months instead of during fall and winter, as is customarily done to reduce salinity in the marsh for migrating ducks and other waterfowl. The Delta smelt relies on low-salinity water – opening the salinity control gates allowed the smelt to enter the marsh from the Sacramento River, where it can access greater amounts of food and shelter.

Extinction looms so closely over the Delta smelt population that the project could have been considered a success even if it didn’t lure any countable Delta smelt to the marsh, said DWR Lead Scientist Ted Sommer. Just creating the conditions that allow smelt to thrive – that is, low salinity levels, lots of food, and high turbidity or muddy water that magnetizes smelt – would have been a cause for celebration.

Conclusion

There are many, many other examples of adverse changes that have put fish population dynamics in the Delta in a perpetual downward spiral. Since 1970, almost of all them involve reduction of Delta inflow and outflow, elimination of measures to mitigate the effects of reduced Delta inflow and outflow, and/or the biological response to reduced Delta inflow and outflow.

Figure 1. State south Delta exports (Harvey Banks pumping plant) in spring 1997-2010.

Figure 2. State south Delta exports (Harvey Banks pumping plant) in spring 2011-2019.

Figure 3. Delta outflow April-May 2007-2009 and 2013-2015 droughts.

 

 

 

  1. Initially exports were even higher with the new 11,000 cfs export capacity of the State Water Project. Total exports reached 12,000-14,000 cfs

Delta June 2019

Water year 2019 has been a very wet year.  Yet salmon and sturgeon survival was compromised by low flows and high water temperatures in the Sacramento River this spring.1 Young salmon survival has been further compromised by low flows, high exports, and high water temperatures in the Delta this past June.

Many of the wild smolts produced in Central Valley rivers this year entered the Delta in May and left (or died) by the end of June, as observed in Delta export salvage collections (Figure 1).  Many of the wild smolts captured in the south Delta likely originated from San Joaquin tributaries.  South Delta exports were near maximum at 10,000 cfs, about 70-80% of San Joaquin inflow to the Delta and 20% of total Delta inflow.  The high exports caused lower flows and associated high water temperatures (>20oC) in the Delta channel of the lower San Joaquin River (Figure 2), and contributed to similarly high temperatures in the lower Sacramento River channel (Figure 3).

The high Delta water temperatures (>20oC) compromised the survival of the salmon smolts in June.  Reducing the export limit to 5000-6000 cfs in June of this wet year would have kept the water temperature near a 20oC limit.  The water quality standards in the 1980’s and 1990’s under D-1485 had a 6,000 cfs June export limit.  In the past two decades under D-1641, the June export limit changed to 65% of total inflow.

New Delta water quality standards should provide export limits and inflow/outflow minimums that protect salmon through the spring months.

Figure 1. Chinook salmon salvage at south Delta export facilities in 2019. Note the prevalence of wild (non-hatchery) smolts in May-June.

Figure 2. Water temperature and tidally-filtered flow at Jersey Point in the lower San Joaquin River channel of the Delta in June 2019.

Figure 3. Water temperature and tidally-filtered flow at Rio Vista in the lower Sacramento River channel of the Delta in June 2019.

 

 

Selective Chinook Salmon Sport Fisheries in Puget Sound With notes on variants for Coho salmon and Steelhead.

Introduction

The Endangered Species Act (ESA) imposed complex challenges to the management of the sport fishery for Chinook salmon in Puget Sound, Washington State. In order to protect limited stocks of “native or wild” Chinook (i.e., those that are not from hatchery origin and naturally spawn in streams), total closures to sport fishing were strongly considered.

Wild and “hatchery” Chinook (i.e., those that are reared in a hatchery) co-mingle in the same Puget Sound habitat. The hatchery fish are often sufficiently abundant in many areas to allow some level of sport fishing. Total closure of the sport fishery for all Chinook was therefore a major issue for sport fishermen because of the high economic value of the sport, the potential overabundance of adult hatchery fish, and the sport of catching this prized species.

To differentiate hatchery from wild salmon, the adipose fin is removed from hatchery-reared smolts before release. Thus, when an angler brings a Chinook to shore or a boat, the angler can visually determine if it is from hatchery origin, based on the absence of this fin. This allows a mark-selective fishery targeting hatchery fish.

Mark-selective Chinook salmon fisheries are sometimes further constrained by “encounter” quotas. In Puget Sound, quotas for angler “encounters” (a combination of legal-size Chinook, wild Chinook, sublegal hatchery fish, and sublegal wild fish) are established annually for 9 specific marine management areas. For selective river fisheries in the Puget Sound area, the encounter approach is not used.

Current management using quotas on catch and encounters allows sport fisheries on hatchery Chinook salmon. Co-managers Washington Department of Fisheries (WDFW) and Native American Tribes use three major methods to manage the Chinook sport fisheries in Puget Sound:

  1. review of angler punch card data,
  2. creel census surveys supplemented with test boat fishing and aerial surveys, and
  3. quotas on encounters in areas of Puget Sound where sublegal and legal sized Chinook salmon co-mingle.

Punch Cards

In addition to a fishing license, anglers fishing for salmon (all species) and certain other species (e.g., steelhead and halibut) must also purchase a punch card. When one of these species is caught and kept, the angler records the date, location, species, and other information on the card. The punch card must be returned to the WDFW at the end of the recording season. If the cards are not returned, there is a penalty charge made on the next license purchased. The card is used to determine annual harvest and historical trends for the various management areas.

Creel Census

To supplement the punch card information, additional “real time” data are monitored through angler “creel” surveys at various sites. These face-to-face surveys collect information on species caught and kept, number of fish released (including any wild salmon, sublegal fish, others species), hours and management area fished.

Encounters

Recording encounters involves the reporting during creel surveys of all Chinook kept and released, including whether fish caught were legal-sized and adipose clipped, legal-adipose intact, sublegal-adipose clipped, or sublegal-adipose intact. Information collected during the creel surveys also records Chinook retained and an estimate from the angler of those that have been hooked and released (legal, sublegal, or native). This information is supplemented by test boat fishing and aerial surveys.

During the pre-season, each of the 9 management areas in Puget Sound is assigned specific seasonal encounter quota numbers. If any of the quotas are reached in an area, that area is closed to further fishing for Chinook.

Discussion

Mark-selective sport fisheries on hatchery salmon in the Puget Sound have been allowed through the use of quotas on angler catch and encounters for specific management areas. The quotas are determined during the pre-season by the fisheries co-managers WDFW and the Tribes. Quotas are derived from a model that includes historical punch card data, spawning surveys from earlier years, and other population and catch data.

The sport fishery for Chinook has severely declined in recent decades. There is a wide array of potential reasons for this decline. These include massive increases in predators (e.g., seals and sea lions), ocean conditions, loss of freshwater habitat, and others. In past decades, fishing for Chinook salmon was open the entire year, with much higher daily limits (up to 3 fish). The fishery has been severely reduced to only a few weeks in summer and limited months in the winter, often with only a 1 fish daily limit. The addition of the encounters approach in recent years has also contributed to large crowds that are condensed into the shortened periods. This, for some, has catching a prized Chinook salmon a lot less enjoyable.

In general, the encounters approach has been useful for allowing Chinook salmon sport fishing to continue on a limited basis while maintaining protections for wild Chinook. There are some drawbacks, however. For example, if the pre-season estimate of Chinook abundance for a particular management area is underestimated, the encounters quota may be reached early and the season closed, even though there may be substantially high survival rates that might have allowed a higher quota value.

Coho salmon and steelhead are also adipose clipped at the hatchery. This allows selective sport fisheries for these species to continue as well, while allowing release of wild spawning adults. However, the encounters methodology is not currently used for these species (capture of sublegal fish is low). In areas where adult Coho populations are low, a selective fishery may occur, in which only hatchery fish are allowed to be retained. However, in areas where populations of “native” Coho are abundant, both wild and hatchery Coho may be kept.

In general, nearly all steelhead management areas in Washington require release of native steelhead, which, in most cases, have a high survival rate when released.

In sum, these mark-selective sport fisheries in Puget Sound allow sport fisheries that otherwise might be banned altogether. Harvest of hatchery fish may also help reduce competition with wild fish for spawning habitat and food resources.