Category Archives: Sturgeon

Sturgeon Moon August 2023

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It is August 2023, and the month will feature two “Super Moons.” The first full moon is called a “Sturgeon Moon,” originally coined in reference to the ease of catching sturgeon in the Great Lakes during a full moon in summer.1 Its cycle began with the quarter moon and neap tide on July 24 until the full moon on August 1.2 This year’s Sturgeon Moon was regrettably prophetic in that it coincided with a new sturgeon die-off in San Francisco Bay in summer 2023.

Last summer, there was die-off of nearly a thousand adult white sturgeon in the greater San Francisco Bay due to a toxic algae bloom. More dead white sturgeon adults have been showing up on Bay beaches again this summer.3 After analyzing data related to the die-off, I now blame the white sturgeon die-off on the Sturgeon Moon (i.e., the tides) and some complicit factors.

Why are toxic algae blooms occurring, and sturgeon dying, again this year, in a wet flood year? Toxic blooms are not supposed to occur in wet years.

Based on the information available, this summer’s die-off event is occurring during a Sturgeon Moon. The Sturgeon Moon cycle (that occurred in late July and early August this year around the August 1 full moon) causes the Delta to rapidly fill from the Bay and stop flowing (termed a spring tide). In the recent heat, all that water in the Delta and lower rivers heated up to 75ºF. Then the Sturgeon Moon cycle drained (neap tide) the Delta into the Bay. When the top three feet or so of warm Delta water all drained into the Bay, it triggered the toxic algae bloom, low oxygen, and hot water. In combination, these factors are killing the fish.

Sturgeon likely suffered their initial stress from the warm lower rivers where they spawned in May. By the time of the Sturgeon Moon, many had moved downstream into the Delta toward the cooler Bay. The emptying of the warm Delta into the Bay during the neap tide likely stimulated further movement into the Bay. Once in the Bay, the stressed sturgeon received added stress from the warm Bay and its new toxic algae bloom and hypoxia conditions. The accumulated stress from the whole series of events likely caused the die-offs observed in the past two summers.

Yes, the Sturgeon Moon, Bay pollution, and algae seeds from last years bloom played a part, but the biggest culprits were state and federal water managers, who allowed the rivers and Delta to heat up in early summer by making high water deliveries upstream of the Delta and exporting high volumes of water from the Delta.

I worry about the accuracy of the loss estimates of adult white sturgeon in the Bay. As noted in the Chronicle article cited and linked above, there may be many dead sturgeon that have gone undetected at the bottom of the Bay. Last year, as many as 1000 sturgeon were found dead. There are probably less than 10,000 adult white sturgeon left in the Bay-Delta spawning population. Sport fishermen generally harvest about a thousand each year. The California Department of Fish and Wildlife and the California Fish and Game Commission are revisiting fishing regulations this fall and may close or restrict the popular sport fishery. 4

Could these circumstances have been avoided? Yes. First by maintaining lower Sacramento River and Delta inflow temperatures (Figure 1) at or below the state water quality standard of 68ºF (20ºC) with adequate flows (greater dam releases and/or less water deliveries). The lower Sacramento River flow of 5000 cfs is far too low for early summer, especially in a wet year. Second, by maintaining Delta temperatures at least in the 20-22ºC range (there is no Delta water temperature standard) with adequate cool inflows. Third, by maintaining water temperatures in Bay below 20ºC with adequate cool Delta outflow during the spring tides. This solution would have been difficult to achieve in drought year 2022, but not in flood year 2023.

Water project managers should have foreseen the tidal patterns coming in the summer (Figure 2) and the inadequacy of the estimated flows they were providing to the Delta (Figure 3). Measured Delta outflow by USGS was actually lower than the DWR model predictions (Figure 4). Instead, water managers provided approximately 20,000 cfs of water deliveries, including near-maximum export pumping from the Delta (Figure 5). The upstream pull to the south Delta export pumps reached a peak near 10,000 cfs in interior Delta channels at the end of July (Figure 6).

The influx of warm water reached a peak at the maximum ebb tide on July 24. This can be seen in Figure 7 at the Carquinez Bridge gage, and Figure 8 in Suisun Bay. Evidence of the Bay bloom can be seen in Figure 9, as the North Bay water returned to the East Bay with its algae (chlorophyll) concentrations and low dissolved oxygen at the end of July, coinciding with the return of the spring tide. Further evidence of the bloom is indicated in Figure 10 in the low nitrogen concentrations at the end of July in Suisun Bay.

In summary, the recent reappearance of a die-off of white sturgeon in the Bay appears to have been triggered by the strong tides of the summer Sturgeon Moon draining warm water from the Delta into the Bay. The warm water, in turn, was the result of excessive water diversions upstream of the Delta and near-maximum water exports from the Delta, combined with tidal dynamics.

Graph showing flow and water temperature in the lower Sacramento River upstream of the Delta at Wilkins Slough (WLK) and at the entrance to the tidal Delta at Freeport (FPT). Red line is water quality standard for lower Sacramento River.

Figure 1. Flow and water temperature in the lower Sacramento River upstream of the Delta at Wilkins Slough (WLK) and at the entrance to the tidal Delta at Freeport (FPT). Red line is water quality standard for lower Sacramento River.

Graph showing Average daily flow and hourly stage at Rio Vista in North Delta near exit to the Bay.

Figure 2. Average daily flow and hourly stage at Rio Vista in North Delta near exit to the Bay. Note the sharp flow increase and the drop in stage on 7/24 (Delta draining under the neap tide of the initial quarter of the Sturgeon Moon.)

Graph showing Stable Delta conditions in July 2023. Inflows = (American River AFO + Lower Sacramento River at Wilkins Slough WLK + lower Feather River at Gridley GRL + lower San Joaquin river at Mossdale MSD. Outflow (DWR-DTO) = Inflow – exports. Note relatively stable conditions.

Figure 3. Stable Delta conditions in July 2023. Inflows = (American River AFO + Lower Sacramento River at Wilkins Slough WLK + lower Feather River at Gridley GRL + lower San Joaquin river at Mossdale MSD. Outflow (DWR-DTO) = Inflow – exports. Note relatively stable conditions. Note DWR outflow is calculated (not measured) from daily flows.

Graph showing Delta outflow as estimated by USGS from flow gages.

Figure 4. Delta outflow as estimated by USGS from flow gages. Note drop in Delta outflow (at the peaks in spring tides) beginning on 7/24 as shown in Figure 2, but not in Figure 3. Also note the peak outflows were higher in USGS outflows.

Graph showing South Delta SWP and CVP exports June-July 2023.

Figure 5. South Delta SWP and CVP exports June-July 2023. Note 20,000 acre-ft per day is approximately hourly average of 10,000 cfs. Maximum export rate is 11,400 cfs (approximately 23,000 acre-ft per day).

Graph showing Old and Middle River flows toward export pumps in south Delta.

Figure 6. Old and Middle River flows toward export pumps in south Delta.

Graph showing Salinity (EC), water temperature (C), and turbidity at Crockett in north Bay in June-July 2023.

Figure 7. Salinity (EC), water temperature (C), and turbidity at Crockett in north Bay in June-July 2023. Note neap tide and lower salinity, warm, clear water on 7/24-25.

Graph showing Salinity (EC), water temperature (C), and turbidity at Port Chicago in east Bay in June-July 2023.

Figure 8. Salinity (EC), water temperature (C), and turbidity at Port Chicago in east Bay in June-July 2023. Note neap tide and lower salinity and warmer water on 7/22-25.

Graph showing Salinity (EC), dissolved oxygen, and chlorophyll concentration in east Bay in June-July 2023.

Figure 9. Salinity (EC), dissolved oxygen, and chlorophyll concentration in east Bay in June-July 2023. Note bloom, higher salinity, low dissolved oxygen beginning on 7/25.

Graph showing Salinity (EC), water temperature (C), and total nitrogen at Pittsburg in east Bay in June-July 2023.

Figure 10. Salinity (EC), water temperature (C), and total nitrogen at Pittsburg in east Bay in June-July 2023. Note higher salinity and water temperature, and reduced nitrogen (from algae uptake) beginning on 7/24-25.

  1. Two supermoons will light up the night sky in August. Here’s what you need to know https://www.sfchronicle.com/bayarea/article/supermoons-two-blue-sturgeon-18270736.php ↩
  2. Spring tides always happen when the Moon is at the full or new phase, which is when the Sun, Moon and Earth are in alignment. Neap tides occur around the first and last quarter phase of the Moon, when the Moon’s orbit around Earth brings it perpendicular to the Sun. ↩
  3. https://www.sfchronicle.com/climate/article/fishkill-18279379.php ↩
  4. https://ncgasa.org/2023/04/17/white-sturgeon-meeting-and-overview-from-cdfw/ ↩

Feather River Salmon Recovery Responsibilities, Commitments, and Recommendations

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

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

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

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

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

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

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

Spring-Run and Fall-Run Salmon Introgression

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

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

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

Lower Feather River Habitat Improvements

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

Flow and Water Temperature

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

Physical Habitat Features

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

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

Benefits to Other Species

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

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

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

Habitat Expansion Agreement – Final Habitat Expansion Plan

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

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

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

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

Summary and Conclusion

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

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

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

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

The Forgotten Green Sturgeon

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Adult Green Sturgeon and General Life History –  Source

The Southern Green Sturgeon is an anadromous fish species that spawns in the upper Sacramento River near Red Bluff CA.  It is a state and federal listed endangered species.  Adults migrate from the ocean to spawn in April-May in gravel/cobble riffles and pools.1  The eggs hatch in approximately 12 days.  The young larval or fry are susceptible to stress and mortality if water temperature warm too quickly into the 65-70oF range.  Optimal water temperatures for embryos and larvae are 60-65oF.2  Survival declines at higher temperatures, with 68oF considered lethal.

The fry grow quickly and begin moving downstream from mid-May to mid-July, as shown by screw trap collections at the Red Bluff Diversion Dam (Figures 1 and 2).  It is the reaches below Red Bluff downstream into the middle river near Wilkins Slough where larvae-fry are vulnerable to excessive spring-season water temperatures.  There are minimal available records of juvenile survival in the middle and lower river, although some data indicate they do not move to the Delta and Bay until the first fall rains.

Juvenile production measured at Red Bluff is lower in drought years (Figure 2) as a consequence of low flows and high water temperatures. With water temperatures already high in early May 2021 (Figure 3), the prognosis for young green sturgeon production is not good.

Figure 1. Screw traps at Red Bluff Diversion Dam in Sacramento River. USFWS photo.

Figure 2. Green sturgeon collections in Red Bluff screw traps 2003-2012. Note poor survival in drought years 2007 through 2009. Source.

Figure 3. Water temperature of the Sacramento River at Red Bluff (RDB rm 240) and Wilkins Slough (WLK rm 125) April-June in 2014, 2015, and 2021. Note the lethal water temperature for green sturgeon larvae is considered to be 68oF.

 

  1. Brown, K. Evidence of spawning by green sturgeon, Acipenser medirostris, in the upper Sacramento River, California. Environ Biol Fish 79, 297–303 (2007). https://doi.org/10.1007/s10641-006-9085-5 ↩
  2. https://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/california_waterfix/exhibits/docs/petitioners_exhibit/dwr/part2/DWR-1102%20Van%20Eenennaam%20et%20al.%202005.pdf ↩

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

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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

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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 ↩