Welcome to the California Fisheries Blog

The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.

Klamath’s Shasta and Scott Rivers – Update Fall 2019

In two May 2017 posts1, I discussed the status of fall-run Chinook salmon in the Scott River and Shasta River through the 2016 runs. This post updates the escapement record for the two rivers through the 2018 runs with preliminary data on the 2019 runs.

Scott River

After a slight uptick in the run in 2017, the Scott fall-run 2018 escapement fell below the 2015-2017 runs (Figure 1); all were affected by the 2012-2016 drought. The run total as of mid-October 2019 was 23. It is too early for a coho update, but the run continues at minimum levels2 with a disappointing strong-brood-year 2016 performance3. A poor 2016 run is likely to lead to a poor 2019 run.

Shasta River

In sharp contrast to the Scott, the Shasta River run continues to improve over its historical record (Figure 2). The run total as of mid-October 2019 was 2,722. The Shasta River coho population remains at critically low levels.

The remarkable recent success of the Shasta River Chinook run from habitat restoration and improvements in water management (and the lack thereof on the Scott River) continues to be undermined by misinformation promoted within the agricultural community. A February 2019 article in the news outlet Grist reported:

In 2016, The Nature Conservancy announced plans to sell Shasta Big Springs Ranch. But without its water, which California Fish and Wildlife still owns, the land isn’t of much use for agriculture. And the fish don’t seem to be doing much better, either — though salmon still spawn at Big Springs, their numbers continue to fluctuate wildly from year to year. It seems that in this ecosystem so changed by people, the salmon need some local stewardship to thrive…

The Scott River remains “the most productive coho stream in California,” according to the nonprofit California Trout. When I spoke to Plank last he told me that the river was splashing. “These fish hatched on this ranch during the last drought,” Plank said. “Today, they’re returning.” [emphasis added]

The article asks the rhetorical question: “So how did such similar conservation efforts go so right at Scott River Ranch and so wrong at Shasta Big Springs Ranch?” For fall-run Chinook, at least, the numbers tell a different story. As for coho, there is no evidence that the population is going anywhere but downhill.

The difference in water management between the two rivers is readily seen in the flow records over the last four years (Figures 3 and 4). The Shasta River has improved flows, whereas the Scott River has had historically low fall flows that keep salmon from ascending from the Klamath to the Scott River spawning grounds. Low summer and fall flows (Figure 3) have also led to very poor survival of young coho and Chinook salmon over-summering in the Scott River.

Figure 1. Escapement of adult fall-run Chinook salmon to the Scott River from 1978 to 2018. Data source: CDFW.

Figure 2. Escapement of adult fall-run Chinook salmon to the Shasta River from 1978 to 2018. Data source: CDFW.

Figure 3. Scott River streamflow 2016-2019. Source: https://nwis.waterdata.usgs.gov/

Figure 4. Shasta River streamflow 2016-2019. Source: https://nwis.waterdata.usgs.gov/



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.


  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

American River Fall-Run Status through 2018

In my August 2017 post on the status of American River fall-run Chinook salmon, I analyzed recruitment through the fall 2016 spawning run. The 2016 run was a product of fall 2013 spawners (brood year 2013). In a May 2019 post, I discussed the survival of hatchery brood year releases through 2014. After record low escapement/recruitment in 2008 and 2009, there was a modest recovery from 2010-2014, followed by lower runs in 2015 and 2016 (brood years 2012 and 2013), the product of the 2012-2016 drought. Brood years 2012, 2013, and 2014 suffered from poor juvenile survival of hatchery and wild salmon in critical drought years 2013-2015. Overall production was sustained by Bay and coastal hatchery smolt releases (trucking and pen releases).

In this post, I update the status of the American River fall-run through 2018 with the addition of escapement estimates for the 2017 and 2018 runs. I also provide updated information on returns of hatchery brood year 2014 (2015 smolt releases). In addition, I provide a prognosis for the fall 2019 and future runs (returns/escapement).

2017 and 2018 Escapement

Poor river escapement in 2017 (Figure 1) likely reflects poor survival of naturally spawned salmon from fall through spring of critical drought water year 2015. The strong hatchery escapement in 2017 (Figure 2) reflects higher survival of brood-year 2014 hatchery releases to the Bay. Escapement improved in 2018 with higher river contributions from brood year 2015.

Updated Brood Year 2014 Hatchery Survival

Survival estimates based on hatchery coded-wire-tag returns for brood year 2014 (released in spring of critical drought year 2015) ranged from 0.3 to 1.4% (Figure 3). All were releases to Bay net pens. The two higher (good) survival rates were from mid-May releases, when outflows were slightly higher and Bay temperatures were cooler (Figure 4). Differences in survival among and within years reflect a positive relationship between survival and Delta outflow on the date of release (Figure 5).

Brood Year 2015 Hatchery Survival

Survival of hatchery brood year 2015 (2018 hatchery counts, Figure 2) was slightly depressed, possibly as a consequence of more of the hatchery smolt production being released into the lower American River rather than trucked to Bay pens (Figure 6). Early tag returns from the 2016 releases indicate much higher survival of the Bay pen releases than river releases (Figure 6).

Prognosis for Brood Year 2016 (Fall 2019 Run)

River flows and Delta outflow conditions were much better in springs of 2016-2019, wetter water years, than in the springs of the 2013-2015 critical drought years (Figure 7). Survival of naturally produced fish and hatchery fish released into the river should show improvements given the wetter conditions. Survival of hatchery fish released to the Bay should be good given higher Delta outflows. It may take wet-year-type spring river flows (Figure 8) or timed pulsed flows to achieve high survival of river smolt releases. River-release survival rates from 2016 and 2018 release groups are likely to be depressed since these water years were saw only moderate flows after mid-April, whereas river-release survival rates from the abundant water years 2017 and 2019 are likely to be good, as in 2010 and 2011.

Figure 1. River spawner estimates 1952-2018.

Figure 1. River spawner estimates 1952-2018.

Figure 2. Hatchery spawner estimates 1955-2018.

Figure 2. Hatchery spawner estimates 1955-2018.

Figure 3. American River Hatchery smolt release group survival (%return) for 2009 to 2015. Data Source: https://www.rmis.org/.

Figure 3. American River Hatchery smolt release group survival (%return) for 2009 to 2015. Data Source: https://www.rmis.org/.

Figure 4. Water temperature and salinity (EC) near American River Hatchery smolt net-pen release sites in spring 2015. Red dots are dates when smolts were released.

Figure 4. Water temperature and salinity (EC) near American River Hatchery smolt net-pen release sites in spring 2015. Red dots are dates when smolts were released.

Figure 5. Smolt Bay-pen release group survival rate versus Delta outflow at the time of release.

Figure 5. Smolt Bay-pen release group survival rate versus Delta outflow at the time of release.

Figure 6. Brood year 2015 hatchery smolt releases in spring 2016.

Figure 6. Brood year 2015 hatchery smolt releases in spring 2016.

Figure 7. Delta outflow spring 2015-2019.

Figure 7. Delta outflow spring 2015-2019.

Figure 8. American River flow at Fair Oaks in spring of selected years in last decade.

Figure 8. American River flow at Fair Oaks in spring of selected years in last decade.



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.


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.


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.


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.


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

Klamath River Salmon – the Wrong Advice!

In a June 2019 article in the LA Times , also posted in Maven’s Notebook, JACQUES LESLIE suggests that “hatcheries don’t belong in this picture” once the planned removal of four dams on the Klamath River is complete.  Based on my decades of work in the Klamath watershed, this post suggests a different approach.  A conservation hatchery could accelerate and improve the outcome of the recovery of Klamath River salmon.  I respond below to a few statements in the article.

“Allowing hatchery salmon to mix with struggling native salmon after removing the dams is like rescuing a dying man only to slowly poison him.”

Native salmon are nearly extinct or already extinct over much of the Klamath River watershed.  A small population of spring-run Chinook remains only in the Salmon River, and is about to be listed as endangered.  Small declining runs of listed Coho salmon remain in several tributaries.  Modest runs of wild fall-run Chinook continue in the Scott and Shasta Rivers, but they are not native to the upper watershed above the mainstem dams slated for removal.  Remaining salmon in the Klamath River are the progeny of hatchery salmon or of interbred hatchery and wild salmon.   Remaining wild Klamath River steelhead are also not native to the upper watershed, and many of them spawn in tributaries downstream of Iron Gate Dam, the lowest Klamath River dam.  Wherever they come from, salmon and steelhead that re-populate the upper watershed will not be native to the upper watershed, at least not initially.

“Salmon hatcheries don’t belong in this picture. They are relics of an outdated worldview that maintains that technology can conquer and control nature. They curtail salmon runs on the river, and instead of diverse stocks of fish that possess varied abilities enabling them to return to spawn — and die — at spots all along the river where they were born, hatchery fish’s birthplace is a single place: the hatchery. The identical life histories of these fish make them more susceptible to disease and predators than their native relatives.”

The modern view of hatcheries, and of conservation hatcheries in particular, is that they (and “technology”) can work with nature rather than controlling it.  One problem is that the life histories of salmon that have survived the dams are not lined up with the likely best life histories for the 400 miles of migration, spawning and rearing habitat of the upper Klamath watershed that will soon become accessible.   Existing life histories of Klamath salmon are lined up with the habitat that was left to them, largely in the few remaining large Klamath tributaries that enter the mainstem downstream of Iron Gate Dam.  Managers of a conservation hatchery can select from the few remaining fish that have the most desirable life histories.  Outplanting these hatchery-bred juveniles in the upper watershed and similar strategies can provide source stock for wild populations that can then better adapt to the habitats of the upper Klamath watershed.

“In fact, maintaining the salmon hatcheries amount to a federal subsidy for commercial and recreational fishing, a subsidy that is supposed to be justified by the fishery’s economic benefits.”

Hatcheries are mitigation for a loss to society and culture, not a “subsidy.”  Those who benefit from the loss commit to paying for the loss.  It is absolutely true that the mitigation has created its own set of problems.  That does not absolve the beneficiaries of responsibility, and it should not disallow the opportunity to improve or accelerate the transition to the robust self-sustaining wild fisheries that every responsible stakeholder seeks.

“The salmon hatcheries on the Klamath should be phased out as quickly as possible. Even if the post-dam comeback of wild salmon is slow, river managers should resist pressure to continue or even expand hatchery operations.”

The hatcheries as they now exist should be phased out if the need to mitigate ends.  Sad thing is that the hydro dams will leave a legacy of degraded habitat and species diversity loss.  It remains to be seen how far habitat restoration can go.  Conversion of the hatcheries to species conservation would help the recovery effort.

In conclusion, a conservation hatchery program could help to restore populations of coho, spring-run Chinook, fall-run Chinook, and steelhead to the areas of the watershed to which dam removal will restore access.  Recovery efforts for native green and white sturgeon, bull trout, redband trout, and suckers could also benefit from modern conservation hatchery programs.  Conservation hatcheries can also preserve the genetic diversity of these native fishes for the future when and if habitat is restored or altered by climate change.