Author Archives: Tom Cannon

2022 Sacramento River Operations – Temperature Management Plan

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So much is at stake in this water year 2022: water supplies, water quality, agricultural production, hydropower production, as well as the future of salmon, steelhead, sturgeon, smelt, and other native fishes of the Klamath and Sacramento-San Joaquin watersheds. Despite the lessons of the 1976-1977, 1987-1992, 2007-2009, and 2013-2015 droughts, the choices and tradeoffs are more difficult, and effects more significant and consequential to the fish, in 2022, the third year of the 2020-2022 drought. The State Water Resources Control Board is about to approve 2022 water operation plans for Central Valley Project (CVP) and the State Water Project (SWP). Among the most immediate effects of these plans will be the fate of iconic fisheries resources of the Sacramento and Klamath Rivers, in 2022 and beyond.

The two key elements of the plans are (1) the Sacramento River Temperature Management Plan (TMP) governing Shasta/Trinity operations, and (2) the Temporary Urgency Change Petition (TUCP) governing Delta operations. A 4/5/22 post covered some aspects of the TUCP on Delta operations, which serves to cut demands on federal and state reservoir storage in the Sacramento River watershed by lowering Delta outflow requirements. (See also CSPA and allied organizations’ protest and objection to the TUCP.)

This post covers the 2022 TMP, which focuses on Shasta/Trinity storage releases and management of Shasta Reservoir’s storage releases and cold-water pool in support of Sacramento River salmon. It starts with a review of both the hydrological and biological effects of Shasta and Trinity operations in 2021. Starting with 2021 creates context in two ways. First, it explains the severe depletion of CVP and SWP storage in 2021, which created the avoidable portion of the extreme storage conditions of 2022. Second, it describes the disastrous failure to protect fish in 2021, both as consequence of bad management and contributor to the dire conditions of fisheries in 2022.

2021 Sacramento River Operations

The predominant characteristic of 2021’s operations of Shasta Reservoir and the Sacramento River was excessive reservoir storage releases over the spring and summer for water deliveries. Within this constrained context, the dominant biological features in 2021 were management of the cold-water pool for salmon , along with associated “downstream” effects on the lower river and Bay-Delta. The 2021 Sacramento River operations plan led to significantly reduced production in brood year 2021 of all four runs of Sacramento salmon.

I have divided the 2021 story into five event periods (Figure 1), each with differing conditions and outcomes:

Period A: The early-April through early-June period was characterized by rapidly rising high releases (6000-9000 cfs) for water deliveries in late April and May. Reclamation claimed it saved 300 TAF of Shasta’s cold-water pool using power bypass of warm surface water for the high spring releases. In reality, the excessive delivery of irrigation water unnecessarily depleted total Shasta storage by nearly 500 TAF and depleted the cold-water pool by 200 TAF. Those storage losses also crippled any ability to subsequently sustain the cold-water pool through the summer.

The releases of unseasonably warmer water (56-60ºF) also (as planned) inhibited spawning in the late-April to early-June portion of the winter-run salmon spawning season (about half of the historical season). It also stressed winter-run and spring-run adults in their upper river pre-spawn holding areas. Recent scientific studies suggest that such stress (extended holding and warmer water) may have contributed to thiamine deficiencies in spawners that contributed to poor subsequent fry survival and smolt production. Rapidly rising flows and water temperatures may have also compromised late-fall-run salmon egg incubation that normally continues into April. Irrigation deliveries in the middle and upper river led to lower flows and high water temperatures in the lower river (Figures 2 and 3); this both reduced the survival of emigrating spring smolts of all four races of salmon, and hindered and stressed upstream migrating winter-run and spring-run adults.

Period B: The mid-June period of cold-water releases (53-55ºF) was designed to stimulate winter-run adult spawning. It also provided 8000 cfs irrigation releases that unnecessarily depleted total storage and the cold-water pool by 6-8 TAF per day for nearly two weeks (~100 TAF lost cold-water pool and total storage). It also resulted in salmon spawning at 8000 cfs, spawning habitat conditions that led to water surface elevations that increased by one-foot and then dropped by two-feet over the summer salmon egg incubation season. I have not assessed the role of flow on the amount of quality spawning habitat available or on the potential of redd dewatering/stranding, although such factors should also be considered in evaluating an operations plan. Irrigation deliveries in the middle and upper river led to lower flows and high water temperatures in the lower river (see Figures 2 and 3), hindering and stressing winter-run and spring-run adults that were late in migrating upstream.

Period C: The late-June to early-August period was the main winter-run egg incubation period under 2021 operations. Flow releases increased to accommodate irrigation demands. Irrigation diversions, in turn, reduced flows in the river further downstream, leading to high water temperatures (72-78ºF) that blocked early arriving fall-run adult immigrants. A rise of almost two feet in water level in early June from the increased flow likely caused some redd scouring in the upper river spawning reach below Keswick Dam.

Period D: The mid-August to mid-September period was characterized by falling storage releases, associated declining water levels, and warming water as the cold-water pool and access to it declined. Winter-run egg incubation continued through the period and likely suffered from stressful water temperatures and redd dewatering. Flows in the lower river increased, and water temperatures declined, becoming less stressful for upstream migrating adult fall-run.

Period E: The late-September through November period was characterized by continued warming of water temperatures due to lessening access to Shasta’s severely depleted cold-water pool, followed by natural fall cooling. Releases and water levels declined rapidly in the spawning reach. At the beginning of the period, warm water interrupted or delayed spring-run and fall-run spawning, while a water level drop of several feet led to redd dewatering and stranding. Winter-run fry were also subjected to potential stranding during the drop in water level. Spring-run and fall-run spawning was likely hindered or delayed into November due to high water temperatures and decreasing flows and associated water levels.

The 2022 Plan

The May 2 2022 Final TMP Is a radical change from the 2021 plan and actual operations. For the first time, Reclamation has prioritized protection of fish over irrigation deliveries to senior Sacramento River Settlement Contractors. The changes also reflect the much lower available storage in this third year of drought (Figure 4). Water release projections are much lower to sustain the cold-water pool and cool downstream temperatures through the summer (Tables 1 and 2).

April Operations and Effects

April operations closely followed the draft plan that Reclamation submitted to the State Water Board on April 6. April operations using middle TCD gates and small imports of Trinity River water maintained Keswick releases at 52-53ºC and 3250 cfs per the draft 2022 TMP. Such operation helped preserve Shasta storage and the volume of the deeper, cold-water pool (<50ºF). Valley-wide precipitation since mid-April increased flows in the middle and lower Sacramento River, stimulating juvenile salmon emigration and adult spring-run and winter-run salmon immigration. A small pulse flow from Keswick to the 30 miles of spawning and rearing habitat below Keswick Dam would have helped stimulate and benefit these salmon migrations, especially those from the upper 30-mile reach that saw little or no benefits from the April storms, but this did not occur.

The draft TMP (April 6) had the same proposed releases from Keswick Reservoir as the final TMP (May 2). However, the end-of-September storage in Shasta Reservoir predicted in the final TMP (1135 TAF) is over 100 TAF lower than was the prediction in the draft TMP (1250 TAF).

Proposed May Operations

The proposed May 4500 cfs release would come from Shasta Dam’s middle gates with access to warmer surface water in the lake, thus saving some of the cold-water pool. Such savings would require warmer releases that would delay spawning and stress holding adult winter-run and spring-run salmon.

For those winter-run who do spawn in May, egg survival could be compromised by the warmer water. With warming surface waters and warmer reservoir inflows in May, and more pre-spawn adult salmon arriving in the 10-mile spawning reach below Keswick Dam, a Keswick release temperature maintained at or below 51ºF would ensure the 10-mile spawning and holding reach is maintained near 53ºF. A colder release would require proportionately more cold water be released from deeper dam gates.

In reality, middle gate operation through early May (Figures 5 and 6) has sustained cooler-than-expected daily-average release temperatures at 51-52ºF. Hydropower peaking has accessed the warmer upper layers of the reservoir (Figures 7 and 8), saving some of the cold-water pool as planned. However, middle-gate operation under hydropower peaking, and gradual warming of reservoir surface waters, will result in increasing release temperatures per the plan later in May. A rapidly warming reservoir may necessitate use of lower gates or less hydropower peaking operations to maintain <54ºF through May per the plan. If spawning commences in early May due to cooler than planned dam releases, higher late May release temperatures would begin to compromise earlier-spawned egg survival. This should cause some re-evaluation of the plan.

Proposed June-September Operations

The proposed June-September 4500 cfs release (4000 cfs in September) from Shasta Dam will be from the lower TCD gates from the cold-water pool at ~50ºF (Table 2). Slightly higher Keswick Dam release water temperatures are predicted due to warming in Keswick Reservoir at ~4500 cfs through-flow. Water temperatures 5 miles downstream at Highway 44 will increase slightly more due to warm air temperatures.

The final temperature management strategy, based on recommendations received from the Sacramento River Temperature Task Group (SRTTG), is to target 58ºF at Highway 44 during the initial part of the season and then target 54.5ºF for 16 weeks around the estimated peak spawning date of Aug 2. This would result in targeting 54.5ºF from June 7 through September 27 or until the cold water is used up. Due to the limited available control in operating the middle gates (as described above), temperatures in June and July may be cooler than 54.5ºF. Reclamation will operate the TCD to target as close as possible to 54.5ºF to conserve cold water for maintaining target temperatures throughout the critical period.

Reclamation also received feedback from SRTTG members that an initial target of 58ºF would help to conserve cold water for later during the more critical portion of the temperature management season. The problem with this is that it will delay spawning, stressing yet-to-spawn adults and compromising survival of earlier-spawned embryos.

Fall Operations

Fall operations will be similar to those described above for Period E in 2021, with the exception of a lesser drop in flow. Water temperatures in late summer and fall will increase as the cold-water pool is depleted and access to it ends. Increasing temperatures will delay spring-run and fall-run spawning and stress pre-spawn adults (potentially aggravating the thiamine deficiency problem).

Uncertainties

The planners have noted significant uncertainties that will require intensive real-time operations and management throughout the summer to achieve the various goals and targets throughout the system. To address uncertainty, Reclamation has employed conservative estimates of future conditions in the modeling assumptions (e.g., hydrology, operations, and meteorology) and projections, and has included as part of the TMP the potential to make changes, in consultation with the SRTTG, Water Operations Management Team, and/or the Shasta Planning Group. The State Board and NMFS should be included in the decision process.

Infrastructure limitations

The 2022 TMP was developed in consideration of the limitations on using the TCD and the need for temperatures below 56ºF at the Livingston Stone National Fish Hatchery. Efforts to address these limitations should be accelerated. Hydropower peaking operations changes should also be considered.

Related Actions to the Final 2022 TMP

1. Six-Fold Increase in Winter-Run Hatchery Smolt Production
Reclamation plans to fund a six-fold increase in the production of hatchery winter-run smolts this year with staged fall-winter releases from the hatchery and Battle Creek. Such releases should timed to coincide with natural flow pulses and pulse flows from Keswick Dam.

2. Transfers of Adult Salmon
The plan includes the capture and transport of adult winter-run salmon to the headwaters of Battle Creek. Good additional measures would be to give these adult fish thiamine injections and to enhance spawning gravels in Battle Creek as soon as possible.

3. Thiamine Treatments
Stresses imposed prior to spawning (e.g., delayed spawning, low flows, warm water during migration) and holding contributes to thiamine deficiency and high mortality of yolk sac fry, both in hatcheries and wild salmon1. Only hatchery salmon can be treated effectively at adult or egg stage, so efforts should be made to treat any wild adults that are handled, as well as to minimize pre-spawning stresses (e.g., erratic flows and high water temperatures).

4. Water delivery cut to 18% to Settlement Contractors
The TMP proposes to limit water deliveries to Sacramento River Settlement Contractors to 18% of their contracted amounts. The State Board should enforce this limitation. Reclamation should subordinate the timing of water releases to contractors to the needs of salmon downstream of Keswick Dam.

5. Reduced Downstream Deliveries
Demand on Shasta storage for Delta inflow/outflow has been reduced by relying more on other SWP/CVP and non-project reservoirs. However, lower Sacramento River and Delta inflows have reached water temperatures above 65ºF in early May, which puts additional stress on salmon that are immigrating in late spring. It is not a question of whether in May or June lower river water temperatures will exceed 68ºF – the state standard – but when.

6. System-Wide Water Management
Reclamation plans to manage system water supplies to minimize demands on Shasta’s cold-water supply. The Plan and temperature modeling relies on numerous drought actions throughout the Sacramento watershed to reduce reliance on stored water from CVP and SWP reservoirs this summer. “These drought actions have added a degree of flexibility to manage storage at Shasta, Oroville and Folsom reservoirs for meeting public health and safety needs, repelling salinity in the Delta, producing hydropower and providing additional cold water for fishery protection throughout the summer.” In 2022, Reclamation has finally cut deliveries to Sacramento River Settlement Contractors substantially below minimum amounts stated in contracts, in order to protect salmon. However, DWR has not done so for Feather River Settlement Contractors. Reclamation and DWR should be looking at system-wide delivery reductions. Reclamation should also call on New Melones for Delta salinity control as needed. See also NRDC et al. Objection to the TMP (May 6, 2022) for additional recommended system measures.

7. Real-Time Adjustments and Reporting
“Daily releases may vary from these flows to adjust for real-time operations. Significant uncertainties exist within the forecast that will require intensive real-time operations management throughout the summer to achieve the various goals and targets throughout the system.” Reporting, scrutiny, and decision making should be open processes.

8. Restoration of Salmon Upstream of Dams
Reclamation is committed to restoring endangered salmon to their historical habitat upstream of Central Valley rim dams. This program should be accelerated.

Tables 1 and 2 are copied directly from the Final TMP dated May 2, 2022.

Figure 1. Keswick Dam release water release rate and temperature, April-November 2021. Five general periods (A-E) are depicted, based on flow-temperature conditions as described in more detail in text. A. Spring high storage release rate (6-9K cfs), including extensive power bypass releases of warm surface water. B. A late-June cold water release to stimulate winter-run salmon spawning (<53ºF). C. A post-spawn higher irrigation release period with late-egg-stage sustaining water temperatures. D. Cold-water pool saving period with falling flows and higher water temperatures. E. Early fall period with loss of access to cold-water pool and reduction in storage releases.

Figure 2. April-December 2021 Sacramento River flow below Keswick Dam (river mile 300) and below Wilkins Slough (river mile 120). The difference between the two locations, plus tributary and ag return inputs, equals total irrigation deliveries via surface diversions and ground water depletions.

Figure 3. Water temperature in the lower Sacramento River at Wilkins Slough (river mile 120) May-August 2021, along with average for past 13 years. Note that the state’s year-round water quality standard for the lower Sacramento River is for water temperature to remain below 68ºF. Water temperatures above 65ºF are stressful to migrating juvenile and adult salmon. Water temperatures above 70ºF hinder adult salmon migration. Water temperatures above 75ºF are lethal to salmon.

Figure 4. Shasta Reservoir storage in 2022 and other selected years.

Figure 5. Shasta Reservoir water temperature profile at end of April 2022.

Figure 6. Water temperatures of Shasta and Keswick Dam releases in 2021 and to date in 2022.

Figure 7. Hourly water temperature in Shasta Dam releases, 4/27-5/7 2022.

Figure 8. Hourly Shasta Dam flow releases 4/27-5/7 2022.

  1. Adult salmon thiamine stores reduce most during the pre-spawning fast (Vuorinen et al. 2020).  Vuorinen PJ, Rokka M, Ritvanen T, Käkelä R, Nikonen S, Pakarinen T, Keinänen M. 2020. Changes in thiamine concentrations, fatty acid composition, and some other lipid-related biochemical indices in Baltic Sea Atlantic salmon (Salmo salar) during the spawning run and pre-spawning fasting. Helgol Mar Res. 74(1):1–24. doi:https://doi.org/10.1186/s10152-020-00542-9. (Crossref), (Web of Science ®), (Google Scholar) https://hmr.biomedcentral.com/articles/10.1186/s10152-020-00542-9 ↩

NOAA Advocacy under ESA

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On March 31, 2022, the Delta Independent Science Board (ISB) met to discuss: “How the State Water Project and Central Valley Project comply with the Endangered Species Act.”  Cathy Marcinkevage, Assistant Regional Administrator in the California Central Valley Office of the National Oceanic and Atmospheric Administration, NOAA Fisheries division, provided an overview of the federal Endangered Species Act (ESA) and the ESA Section 7 consultation process between NOAA and the Bureau of Reclamation regarding the effects of the Central Valley Project (CVP).

During questions, the ISB’s Dr. Robert Naiman asked if NOAA has “…the legal clout to require dams and other water diversions to install fish passage facilities.”  He provided context, observing: “…[N]one of the dams within the Delta’s watershed have fish passage facilities, and yet you have endangered species that could use the habitat above the dam, assuming you can get them through…” Naiman also noted: “In the Pacific Northwest and elsewhere, there have been a lot of retrofits for fish passage facilities as well as retrofits for regulating water temperatures in the rivers.”

In response, Ms. Marcinkevage spoke to NOAA’s authorities pertaining to fish passage at CVP dams.

First, she mentioned NOAA’s technical criteria for fish passage at intakes at diversion dams’ structures, for example the specifications along the surface of a fish screen: “We do have passage criteria for projects in terms of sweeping velocity and things like that.”

Second, she identified NOAA’s authorities under the Federal Power Act to prescribe fish passage at hydropower facilities (which all major Central Valley dams have).  However, this law does not pertain to federal dams, including the CVP dams.

Third, she said that NOAA, under the Federal Endangered Species Act (ESA), can be an advocate during ESA consultation with federal agencies: “With Section 7, we can try to advocate and get projects to do things within our needs.” [Emphasis added]

This is where we take issue with Ms. Marcinkevage.  Under the ESA, NOAA is clearly more than an advocate.  The agency has the principal regulatory authorities and responsibilities to protect and recover ESA-listed anadromous fishes.

NOAA’s job in a Section 7 consultation includes analysis of a project (action) as proposed, which Ms. Marcinkevage described: “But our job there is to analyze the project as it has come to us and identify its likelihood of jeopardizing the species.”  However, the ESA consultation process often also requires changing the details of the proposed project if necessary so that the project complies with the ESA.

Furthermore, NOAA must analyze the effects of a proposed action in the much broader context of the past and present baseline effects, to which a proposed action’s effects are added.  The baseline geographic reach and scale of the CVP are vast.  The CVP was and continues to be a major source of “stressors” that led to the ESA listing of multiple salmon, steelhead, sturgeon, and smelt species, including most of California’s anadromous fishes.

In addition to the large-scale hydrologic influences exerted downstream of the CVP impoundments, CVP dams were constructed with no fish passage facilities.  As a result, part of the CVP baseline is complete blockage of anadromous fish for decades, extending to the present.  Without access, vast amounts of habitat capacity and habitat diversity of anadromous fishes have been lost.

Dr. Naiman noted that endangered fishes could potentially use the habitat above the dams. Dams constructed with no fish passage are not unique to California, and the biological consequences they impose are well understood.  Salmon populations blocked from their historical habitat suffer devastating losses of abundance, productivity, and spatial diversity. These well-known facts were most likely what prompted Dr. Naiman’s question about NOAA’s legal authorities to require fish passage.

The ISB can and should be asking if it is possible to recover the salmon populations by “fixing” rim dam infrastructure and operations, and lower river and Bay-Delta habitats and water diversions, without fish passage past rim dams.  Stated another way, is recovery even possible in the absence of restored passage to historical anadromous habitats above the dams?

Ms. Marcinkevage suggested that NOAA can “work out” with the action agency alternatives to a proposed action that blocks or impairs fish passage:

“Now, as we do that [analyze the project], if we were to find that this project will continue to be a barrier or impose a barrier that will impede passage, we could work out an alternative that would prevent that.”

To date, nowhere in California’s Central Valley has NOAA performed an evaluation of a dam, found it to be a barrier to anadromous fish passage, and worked out a solution to the blockage of fish migration.  As Dr. Naiman observed, none of the major dams within the Delta’s watershed provide fish passage.

Clearly, NOAA has ESA authority to require alternatives to avoid jeopardy.  Exercise of this authority gets closer to Dr. Naiman’s question about the agency’s “legal clout” to require fish passage facilities.  Ms. Marcinkevage’s response did not differentiate between reasonable and prudent measures (RPMs), and reasonable and prudent alternatives (RPAs) in an ESA biological opinion.  RPMs are voluntary on the part of the action agency, while RPAs are NOAA-enforceable, and could include fish passage requirements.

Ms. Marcinkevage expressed a frank opinion about how to go about creating fish passage over CVP dams:

“But there’s something to not wanting to come in and being the completely authoritarian with the heavy regulatory hand to impose something that, frankly, can’t be done, but rather work out a more workable solution.”

Has NOAA concluded that passage over the CVP dams can’t be done?  The 2009 salmon Biological Opinion for the CVP included an RPA that required fish passage at Shasta and Folsom reservoirs.  It was that requirement that leveraged NOAA, in 2017, to conduct a test in Shasta Reservoir.  The test released juvenile salmon in the McCloud Arm to understand their ability to transit Shasta Reservoir during a wet water-year’s higher flows.   ~70% of the test fish reached the Dam.  A much lower transit success (~1%) occurred in a second experiment undertaken during an average water-year.  These are hardly unexpected results, given the enormity of Lake Shasta.  In order to capture emigrating juvenile salmon with high efficiency, head-of-reservoir collectors (rather than collectors at the dams) are sometimes deployed in Pacific Northwest reservoirs, although the reservoirs are much smaller than Shasta.

In 2019, the Trump administration stopped NOAA’s fish passage efforts at Shasta in their tracks.  The bogus Trump 2019 BiOp for the CVP eliminated the RPA that required fish passage.  And Trump’s Forest Service administrators ordered NOAA to not use Forest Service land for fish passage actions.  Now, NOAA will be conducting further studies in 2022 or 2023 to evaluate head-of-reservoir collection of downstream-migrating juveniles where the McCloud River enters Shasta Reservoir.  Though these studies are as yet voluntary, there is a fair likelihood that the forthcoming new salmon Biological Opinion will restore the fish passage RPA.

Notwithstanding NOAA’s preference to avoid a “heavy regulatory hand” under its ESA authority, the agency is entrusted with legal responsibilities to protect and recover listed species.  Enacting “collaborative,” less controversial mitigation alternatives at Battle Creek led to 20 years of delay in removing, or putting fish ladders over, only some of the small hydropower dams on Battle Creek that PG&E has now decided to abandon.  And in any case, recovering listed Central Valley salmon species without fish passage to major watersheds upstream of Central Valley rim dams is unlikely.

NOAA’s Recovery Plan for ESA-listed Central Valley salmon calls for at least three viable and spatially-diverse winter-run Chinook populations to recover the species.  If that’s to be accomplished, fish passage investigations at Shasta Dam need to be carried out and completed with haste.  The alternative is for the public to enlist the judicial system to provide the “heavy hand” needed for effective application of the ESA to protect our public trust resources.

Smelt Status – Spring 2022

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Initial 2022 late winter surveys indicate modest improvement in longfin and Delta smelt populations. Previous posts outlined the grim status of the two species.1

Delta Smelt

Five larval Delta smelt were captured in the first 20-mm survey of 2022. They were captured in the Cache Slough Complex in late March (Figure 1). After more of the survey is processed, further numbers of recently hatched larvae may be noted, indicating a slight improvement in the nearly extinct population.

Longfin Smelt

Larval longfin smelt were widely collected in the late February Smelt Larva Survey (Figure 2). Highest densities were in the low-salinity zone (Figures 2 and 3). Numbers were higher than in recent years, likely reflecting good early winter condition after high December Valley-wide precipitation.

These modest improvements in the endangered smelt populations will likely be short-lived as the State Board enacts the Temporary Urgency Change Petition (TUCP) of the Department of Water Resources and the Bureau of Reclamation in response to the winter 2022 drought. The TUCP will further reduce freshwater outflow and move the low-salinity zone upstream into the Delta (Figure 4 and 5). Depleted reservoir storage resulting from excessive storage releases to water contractors in 2020 and 2021 created the need for the petition. Despite the depleted reservoir storage, less extreme measures are possible that would provide some protection for the smelt, as discussed in an April 5 post.

Figure 1. Partial results of late March 2022 20-mm Survey, showing location of 5 identified Delta smelt larvae in Cache Slough Complex.

Figure 2. Results of late February 2022 Smelt Larva Survey, showing density of longfin smelt larvae collected in Bay-Delta survey region. Red outline is area of low-salinity zone (2000-8000 EC).

Figure 3. Plot of longfin smelt larvae catch per 1000 cubic meters sampled in late February Smelt Larva Survey (shown in Figure 2). Red curve shows that larvae were concentrated in the low-salinity zone (2000-8000 EC).

Figure 4. Salinity at confluence of Sacramento and San Joaquin Delta channels in eastern Suisun Bay in late winter – early spring 2022.

Figure 5. Calculated Delta outflow in late winter – early spring 2022.

A Simplified Look at the Complex World of Fish Population Dynamics

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I have a simplified approach in analyzing fish population dynamics from which I review the status of populations of smelt and salmon. It looks at the dynamics of the relationship between the number of spawning adults and their returning adult recruits one to several years later (Figure 1). In the fish science vernacular, it is sometimes referred to as the “spawner-recruit curve” or “stock-recruitment relationship” or simply “S/R relationship”. The major features of a S/R relationship are shown in Figure 1 (A, B, and C):

A. The blue and red curves show a standard spawner-recruit relationship, with higher spawners bringing more recruits – more eggs, more young, more smolts, more returning spawners, etc. It tails off when too many adults result in competition for food or spawning habitat, or higher rates of communicable disease – density-dependent effects.

B. The variability around the blue and red curves, shown by the vertical lines through the curves, is caused by density-independent effects such as drought, fishing harvest, or pollution that vary from year to year.

C. The difference between the blue and red curves, shown in the example as a yellow arrow, is a shift in the S/R curve that is a result in a fundamental shift in the relationship. Examples of such changes are the amount or quality of habitat from a dam being built, watershed destruction from a fire, loss of streamflow from new water diversions, loss of prey base, etc. The blue curve shows the S/R relationship before a fundamental shift; the red curve shows the S/R relationship after the fundamental shift.

Some environmental factors can affect one or more of the three features. For example, hatcheries can increase recruits (A and B), or they can cause a fundamental shift in the relationship (C) by imposing genetic changes in the population. Hatcheries benefit egg viability and fry survival, producing more smolts to the ocean per spawner in salmon populations, but may alter the wild component’s genetic viability.

The winter-run salmon population’s S/R relationship (Figure 2) exhibits these features, as well as the overall complexity in the relationship. Hatchery smolt introductions have propped up the population over the past two decades and increased its variability (red curve and vertical line), especially during periods of drought.

For longfin smelt, a state-listed species, there is a strong S/R relationship (Figure 3) to the features described in A-C above. There is a strong positive S/R relationship (A). There is a strong effect of the climate (B). And there appears to be a fundamental shift in recent years (C).

For Delta smelt (Figure 4), a state- and federally-listed species, which I consider nearly extinct at least in the wild, there was a strong S/R relationship (A), a climate effect (B), and a fundamental shift (C). The latter proved simply not sustainable, leading to a population crash that is not recoverable without supplementation (hatchery inputs) or drastic changes In environmental conditions.1 Note that 2016 is the last year in this figure, because the population since 2017 has been too close to zero to evaluate.

The largest salmon population, the Sacramento fall-run salmon, long sustained by hatchery inputs, is mainly controlled by feature B (Figure 5). Climate and water management are the dominant control of survival of hatchery and naturally-produced smolts reaching the ocean.

In conclusion, I recognize that S/R relationships represent a simplified view of extremely complex and changing relationships in the real world. Estimates of the number of spawners and recruits are often crude. But the relationships are real and statistically significant. It is up to us to interpret them by relating causal factors and developing hypotheses that can be tested with further scientific study and experiments. Unfortunately, managing fishery resources in the face of complex ecology, difficulty monitoring, natural variability, and statistical measurement errors is inherently difficult, even before political and economic factors get into the mix.

Figure 1. Spawner-Recruit relationships with three main features (A-C). See text for explanation of the features. In figures 2-4 below, the blue curve represents the historical S/R relationship. The red curve represents the new historical S/R relationship following a fundamental shift in the relationship, including long-term drought. The vertical lines through the curves show the range of the annual variability of the S/R relationship attached to each curve, excluding the density-dependent variability that is incorporated into the curve. In this example figure, the yellow curve tracks a fundamental shift in the S/R relationship. Spawners are shown on the x-axis; recruits are shown on the y-axis. The numbers on the axes are log transformed in order to make size of the figures manageable; log transformation does not alter the statistical relationships.

Figure 2. Spawner-Recruit relationship for winter-run Chinook salmon in the Sacramento River. Numbers shown represent the brood year of recruits (number of returning adults) for year displayed. For example, “11” represents fish produced in wet year 2011. The color of the number shows the conditions when brood was spawned and reared in the upper Sacramento River below Shasta Dam before emigrating to the ocean. A red number shows a dry year during spawning and early rearing. A blue number designates wet year spawning and rearing conditions. A green number designates normal water year conditions. For example, 15 represents brood-year 2015 recruits that returned in 2018, while its red color designates drought conditions in 2015. In this figure, numbers on axes are log-2 transformed.

Figure 3. The longfin smelt S/R relationship. The number and color represents the brood year’s fall index (recruits) and its water year type during its spawning run and first year of rearing. The spawners are the index from two years earlier. For example, the red number 15 represents the fall index for brood-year 2015 under water-year 2015 drought conditions, with spawners being the recruits from 2013. In this figure, numbers on axes are log-log transformed.

Figure 4. The Delta Smelt S/R relationship. I added two curves and a vertical line to an original figure to show the hypothesized S/R relationship; there is too little variability in the red curve for a vertical line to be meaningful.

Figure 5. Spawner-Recruit relationship for upper Sacramento River mainstem fall-run Chinook salmon. Number is recruitment year (escapement). Spawners are recruits from three years prior. Numbers are log minus 3 transformed. A red number shows a dry water year two years prior during rearing and emigration. A blue number shows a wet year two years prior. A green number shows for a normal water year two years prior. For example: red 17 represents 2017 run that reared in drought year 2015, with spawners (parents) being the 2014 green run number. Note that only one curve is shown. in gray, for this run of salmon, which is almost entirely dependent on hatchery production.

Water Projects’ Temporary Urgent Change Petition 3/18/22 Comment on Provision #1 – Spring (April-June) Delta Outflow and Salinity Intrusion

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The U.S. Bureau of Reclamation and the California Department of Water Resources (Reclamation and DWR) filed a “Temporary Urgency Change Petition” (TUCP) on March 18, 2020.  If granted, the TUCP reduce Delta outflow requirements.  The proposed averaging requirements in the TUCP pose a problem in addition to the problem of too little overall outflow.

The TUCP states:

Reclamation and DWR are requesting to modify certain terms as the Projects’ storage and inflow may not be sufficient to meet D-1641 requirements and additional operational flexibility of the Projects is needed to support Reclamation and DWR’s priorities, which include: operating the Projects to provide for minimum health and safety supplies (defined as minimum demands of water contractors for domestic supply, fire protection, or sanitation during the year); preserve upstream storage for release later in the summer to control saltwater intrusion into the Sacramento-San Joaquin Delta (Delta); preserve cold water in Shasta Lake and other reservoirs to manage river temperatures for various runs of Chinook salmon and steelhead; maintain protections for State and federally endangered and threatened species and other fish and wildlife resources; and meet other critical water supply needs. (3/18/22 TUCP, p. 1)

The TUCP is requesting reduced Delta outflow requirements for the April 1 through June 30, 2022 period, for the stated primary purpose of preserving storage in Oroville and Folsom reservoirs.   What I term Provision #1 is reduction of outflow requirement from 3-day average of 7,6001 to 14-day average of 4,000 cubic feet per second (cfs).

The requirement in Revised Water Rights Decision 1641 of a 3-day average of 7,600 cfs is meant to keep salt water from encroaching upstream from the Bay into the Delta in drought years like 2021 and 2022.   This helps to protect the beneficial uses in the Delta including fish, fish low-salinity habitat, Delta agriculture, and south Delta water export water quality.  The TUCP’s proposed Delta outflow of 4000 cfs is meant to provide minimum protection in the face of low available water supply (reservoir storage and precipitation).

The overriding problem with the TUCP’s proposed flow reduction is that it does not require enough flow.  Yet, even accepting the need to reduce flow to allow storage of more water in Reclamation and DWR’s reservoirs, the requested change could be modified to better protect beneficial uses.

Under past TUCPs, DWR and Reclamation have used the 14-day averaging window to game operations to skate as closely as possible to the edge of compliance.  This has led to erratic outflows, often below 4000 cfs (Figure 1).  More precise estimates taking into account tides show outflow is lower than intended (Figure 2).  In these circumstances, salinity has increasingly moved up from the Bay into the Delta under such minimum freshwater outflow (Figures 3-6).

I recommend the outflow required be more stable, allowing for only minimal salinity increase over the spring.  A 3-day average of 4,000 cfs measured outflow would provide greater protection of beneficial uses.

Salinity criteria are more easily defined and measured, and more directly related to beneficial uses.  Criteria for Collinsville, Emmaton, Jersey Point, and Old River that have a maximum for a 3-day average or a maximum daily level with a minimum increase over the spring would also be more protective.

Figure 1. Daily Delta outflow estimated from measured Delta hydrology conditions in spring 2014, 2015, and 2021, drought years when previous TUCPs were implemented

Figure 2. Measured Delta outflow into Suisun Bay in spring 2021.

Figure 3. Salinity in eastern Suisun Bay in spring 2021.

igure 4. Salinity in lower end of Sacramento River near Rio Vista in late April 2021.

Figure 5. Salinity and net tidal flow in lower San Joaquin River channel at Jersey Point in spring 2021.

Figure 6. Salinity (EC) and net tidal flow in lower Old River channel in south Delta near Byron in spring 2021.

  1. The normal requirements are stated in Revised Water Rights Decision 1641, Table 3, footnote 10, pp. 185-186.  The April-June requirement in a Critically Dry year is also met if either the daily average or 14-day running average EC (measurement of salinity) at the confluence of the Sacramento and the San Joaquin rivers is less than or equal to 2.64 mmhos/cm (Collinsville station C2).  From May 1 through June 30, if the Sacramento River Index is less than 8.1 million acre-feet, the flows requested in the TUCP would be the same as the required flows under Decision 1641. ↩