Science, Management, Issues, Problems, and Solutions
Welcome to the California Fisheries Blog
The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.
In a 10/19/2023 post, I discussed how the lack of access to Folsom’s deep cold-water-pool results in delayed natural and hatchery spawning of American River fall-run salmon. During the 2020-2022 drought, Reclamation released water from the lower-level power bypass to provide the cold water (<55ºF) salmon need for spawning (see Figure 1). However, this fall 2024 Reclamation has chosen not to use the power bypass to release cold water (Figure 2), despite higher storage levels than during the recent drought (Figure 3). Lack of cold water delays natural spawning and hatchery egg taking, to the detriment of egg viability and fry production.
Figure 1. Water temperature of water released from Folsom Dam, Oct-Nov 2021. Late October drop in water temperature was from release of cold water from lower level outlet. Also shown is recent average for previous 7 years.
Figure 2. Water temperature of water released from Folsom Dam, Oct-Nov 2024.
Summer 2024 was an unusual summer in an unusual year for salmon in California’s Central Valley.
July 2024 was the hottest ever recorded on earth and in the Central Valley. Record high air temperatures occurred in early July throughout the Valley. A close look at July 2024 provides some valuable insights as to the future climate and salmon in the Valley.
July is an important month for Chinook salmon populations in the reaches of the rivers that are downstream of major dams. Winter-run salmon are at peak spawning in the Sacramento River near Redding (mainly the ten miles below Keswick Dam). Spring-run salmon are holding over the summer in the Trinity River below Lewiston Dam, in the Sacramento River below Keswick Dam, and in Clear Creek below Whiskeytown Dam. (Spring-run salmon are also holding in the Feather River below Oroville Dam and below falls on Butte, Deer, and Mill creeks.) Fall-run salmon have only just begun their journey from the ocean in the Sacramento and Klamath/Trinity rivers.
The goal in summer for the Shasta/Trinity Division of the federal Central Valley Project is to keep dam releases cold (around 50-52oF) for winter-run spawning and egg incubation, and for holding adult spring-run salmon. Dam releases from the stored cold-water-pool supply are prescribed to accomplish the goal. The dams also release water for hydropower, for downstream water supply deliveries, and to meet requirements for salmon habitat and other environmental purposes.
Reclamation must balance these uses in July with protecting the salmon and other fish during the rest of the water year and with maintaining adequate storage for next water year. Reclamation released its draft environmental impact statement for the future long-term operations of the Central Valley Project operating earlier this summer – comments were due in September. Reclamation’s plan is not to meet the needs of the salmon except in wetter years – simply put, to “split the baby.” Reclamation’s proposal for how it will balance the needs of water users and the salmon will lead to the extinction of at least two runs of the salmon.
In the Central Valley, Water Year 2024 turned out to be above normal, after a wet 2023. Shasta and Trinity reservoirs nearly filled during the winter-spring – a good start to end-of-spring conditions. Shasta Lake started July with 4 million acre-feet (maf) in storage (out of a 4.5 maf capacity) and ended July with storage of 3.5 maf (Figures 1 and 2). Trinity Lake began and ended July with 2 maf in storage (out of a 2.5 maf capacity), after transferring about 100 thousand acre-feet (taf) to the Sacramento River in May-June and another 100 taf in July. Water temperatures of released water from both Keswick and Lewiston dams were maintained at the target 50-52oF. The secret to this success was retention of sufficient storage and cold-water pool supplies in Shasta and Trinity reservoirs – a relatively easy task in an above normal water year after a wet year.
The challenge for Reclamation in the past, present, and future is to retain sufficient storage and cold-water-pool supplies to maintain the 50-52oF dam release targets through the fall of all water year types, especially the drier years. Reclamation tried in the 2021-2022 drought, but grievously failed to meet the needs of salmon (Figures 2-4). Now Reclamation is asking the state and federal resources agencies for permission to explicitly plan to not meet the needs of the salmon in drier years.
Absent such an agreement to fail in drier years, Reclamation will have to reduce hydropower production/revenues and, most critically, the amount of irrigation deliveries to water contractors. It will have to reduce already dry-year-constrained water deliveries to retain more stored water and the necessary cold-water-pool supply for salmon. It will have to carry over more storage supply at the end of summer, have greater amounts stored by the end of spring, and deliver less water in many years from spring through fall. There is no choice if Reclamation is to meet promises and commitments to maintain the salmon populations in the Klamath/Trinity and Central Valley.
For a more insight on what the plan entails and how better to meet the needs of salmon, see CSPA’s alternative plan submitted in 2021 to save salmon in a drought year like 2021.
Figure 1. July 2024 conditions in the Shasta-Trinity Division of the CVP. Blue numbers are streamflows (cfs) and reservoir water storage levels. Green numbers are average water temperatures (degrees F).
Figure 2. May-October Shasta Reservoir storage levels in acre-feet 2021-2024.
Figure 3. Trinity River flows and water temperatures below Lewiston Dam 2020-2024.
Figure 4. Water temperature of Sacramento River below Keswick Dam 2021-2024. Note the cold-water-pool supply in Shasta Reservoir was depleted by the send of August in drought years 2021 and 2022 despite attempts to conserve the supply in spring by releasing warmer surface waters from the reservoir.
The spring-run Chinook salmon in Butte Creek had extremely low spawning runs in 2023 and 2024 (Figure 1).
In part, this was because all Sacramento River Valley salmon populations are collapsing due to the direct and indirect effects of the 2020-2022 drought and related management actions, on top of climate change and catastrophic fires.1 Drought conditions in 2021 and 2022 in the spawning rivers, lower Sacramento River, Delta, Bay, and ocean all contributed to poor juvenile salmon survival.
The poor number of Butte Creek spawners in 2024 is also related to the high pre-spawn mortality of adult salmon in Butte Creek in 2021,2 as a result of drought conditions during the winter-spring upstream migration and summer-fall holding and spawning.
Despite the failures of brood years 2020 and 2021, there is optimism for brood year 2022 and its spawning run in 2025 (Figure 2). Water year 2023 was a wet year, with good young survival conditions for juvenile salmon. Though brood year 2022 had only about 3700 spawners, , the returning adults were able to migrate and spawn with minimal stress in a drought year.
The uncertainty that remains is the survival of brood years 2023 and 2024, because of their potential small number of returning spawners in 2026 and 2027. Water year 2024 was a above-normal water year, but it was not without its stresses.3 Early indicators suggest 2025 could be a dry year. The potential for small runs to lead to strong brood years also leaves room for doubt given that four recent years of poor spawners led to poor recruitment (four dots at lower left in Figure 2).
The poor spawner numbers in 2023 and 2024, coupled with the uncertain forecasts for runs in 2025-2027, represent a serious population threat that calls for strong actions to save the species and rebuilding the spawning stock.
Winter Actions
Winter fry-fingerling emigration down lower Butte Creek past the Parrot-Phelan Diversion Dam and the primary screw trap counting station occurs in earnest beginning in mid-December, with a peak in January. The peak in fry emigration (the main element of juvenile salmon production from Butte Creek) occurs during early winter precipitation events. The fry, often still feeding on their yolk sac, leave the cold turbid creek heading for warmer, low-velocity food-rich floodplain waters of the Butte Basin and the Sutter Bypass, and for the tidewater of the Bay-Delta.
Strong winter growth is essential for good survival (good growth rates, and lower rates of starvation and predation). Strong winter growth promotes early smoltification and entry to the ocean. The main success factors in winter are adequate transport flow, access to and from floodplain habitats in the Butte Basin and Sutter Bypass, and low predation rates.
Spring Actions
Pre-smolt, sub-yearling smolts, and yearling smolts emigrate in modest numbers from Butte Creek in spring. These late migrants contribute to population numbers and genetic diversity. Success of these late migrants depends on high transport rates, low water temperatures, minimal diversion to often excessively warm floodplain habitats, minimal entrainment into unscreened water diversions, and minimum flow-through rates from river to floodplain habitats.
Adult spring-run salmon migrate from the Bay to upper Butte Creek in spring. They require adequate flows and water temperatures often not available in drought years, especially in late spring.
Specific Winter and Spring Actions to Consider:
Minimize water diversions at Parrot-Phelan Diversion Dam (and other creek diversions). In early winter, prioritize flow in Butte Creek over diversions for waterfowl pond flood-up and rice field decomposition (Figure 3), except in high runoff conditions. In spring, maintain flow in Butte Creek at the highest levels possible for attraction and holding except in early spring flood conditions.
Minimize the flow split into Sanborn Slough at bifurcation weir. Do not force more than 30% of Butte Creek flow into Sanborn Slough, which reduces important benefits of floodplain access and inundation.
Minimize diversions in Butte Basin and Sutter Bypass.
Keep Butte Slough Outfall closed except under Butte Creek flood relief conditions; instead, maximize flow through Butte Basin and Sutter Bypass.
In the event of dry-drought conditions, capture juvenile salmon at screw trap locations and Parrot Phelan Screen Bypass, and transport them to the mouth of Butte Creek, Verona, a conservation hatchery, downstream floodplain habitat, or a Bay-Delta location.
Maintain adequate transport flows in the lower Yolo Bypass and lower Sacramento River, and into and out of the Delta in winter, to maximize survival to the Bay and ocean.
Figure 1. Butte Creek spring-run salmon population (escapement or spawning run size) from 1975 to 2024. Red circle highlights dramatic decline in 2023 and 2024.Figure 2. Spawner/recruit relationship for Butte Creek spring-run salmon with three-year lag between spawners and recruits. Numbers shown in chart are return years (recruits). Blue is a wet year two years prior to spawning run when salmon were rearing and migrating to the ocean. Green are normal water years. Red are dry and critically dry years. Year labeled 25 is expected return run in 2025. Purple line is potential range of runs in 2026 and 2027 depending on success of brood years 2023 and 2024.Figure 3. Water diversion rate at Parrot-Phelan Diversion Dam fall 2023 to fall 2024 (water year 2024).
The final steps in Klamath River dam removal are complete, and the first salmon has migrated upstream into the dam-removal reach in over 100 years. The four reservoirs were drained last winter and the dams removed this summer. The river is now free in its natural channel. Two dams remain up at Klamath Lake (Keno and Link dams – not part of the project), but the lower four hydroelectric project dams – three in Oregon and one in California – are gone. With the demolition of the last of these lower four dams this summer, the Klamath is running free from its headwaters in southeastern Oregon to its mouth in the Pacific Ocean on Yurok tribal lands in northwestern California. Hundreds of miles of spawning grounds are open to Chinook salmon, Coho salmon, and steelhead for the first time in more than a century.
The dam-removal process was not without problems, although these problems were generally foreseen in planning and permitting. First was the reservoir draining process this past winter, when the reservoirs were drained, from mid-January to mid-February. In the four-dam reach and in the Klamath River downstream, high suspended fine sediment and low dissolved oxygen were problems, though determined of limited risk to the few salmon and steelhead in the river at that time. However, the Assisted Sediment Evacuation project element (Figure 1) continued past its prescribed end date of March 15 into early April, extending the presence of lethal levels of suspended sediment into the early juvenile salmon and steelhead emigration season from tributaries, a season that includes March. Lethal levels of suspended sediment extended downstream over 100 miles as far as Orleans (Figures 2 and 3).
Subsequently, during the summer, dam infrastructure was removed to provide full salmon passage past the dam sites. Low flows necessary to access the dam sites for material removal, and high summer air temperatures, resulted in very warm water temperatures beginning in July. Removal of coffer dams and further Assistant Sediment Evacuation at the dam sites (Figure 4) led to the return of lethal sediment levels in the river below Iron Gate (see Figure 2). On three days, dissolved oxygen below Iron Gate reached zero.
Though approved by the project technical team, the high suspended sediment level through September likely hindered a major portion of the fall-run Chinook salmon run up the Klamath River (Figure 5). Only 60 adult salmon were reported at the Shasta River trap as of early October, by which time daily numbers are usually in the hundreds. Numbers at other traps at other tributaries were even lower, which perhaps explains why only one salmon has been seen at the new sonar station above the Iron Gate Dam site.
With the cessation of Assisted Sediment Evacuation at the end of September, the hope is that suspended sediment levels will return to the low pre-summer levels and fall-run Chinook salmon will recommence their migration upriver. The river should be clear for late fall and winter runs of coho salmon and steelhead.
The use of Assisted Sediment Evacuation in winter and early spring, and then again in late summer, will remain controversial, if only in that it was applied under an extended time frame from the original planning and permitting documents. The summer application was certainly a surprise to local stakeholders,1 who were shocked by the extent and duration of the muddy and smelly river conditions. A condition of zero dissolved oxygen for 50 miles below Iron Gate dam for two days in September was not approved under the permits issued by the state or federal governments.
In my opinion, the initial and final evacuation of muddy sediment should not have been implemented by using excavators to dump sediment directly into the river. A better option would have been natural removal by winter storm events that would have provided a much higher dilution factor and would have had a better chance for a non-lethal concentration of suspended sediment. Furthermore, more of the sediment should have been removed or stored in upper terraces and not allowed to enter the river.
The NOAA Fisheries final assessment of the dam removal effort failed to acknowledge the problems and potential consequences of the spring or summer events.
“Heavy equipment removed the final obstacle separating the Klamath River from the Pacific Ocean on Tuesday. The reconnected river was turbid but remained safe for fish after crews took steps to avoid erosion and impacts to water quality.” The river was not safe for salmon or steelhead for over 100 miles downstream.
“Crews used a strategy of releasing sediment and organic material that muddied the river but avoided a decline in dissolved oxygen that could have otherwise harmed fish.” Untrue. Both dissolved oxygen and suspended sediment levels were lethal. Hopefully, many fish were able to avoid these conditions.
Figure 1. Photo of Assisted Sediment Evacuation process from Iron Gate Reservoir in March 2024. (KRRC video screengrab)Figure 2. Turbidity (as measured in FNUs) in lower Klamath River in 2024. (Karuk water quality data). See Figure 3 for locations. Red line is approximate lethal concentration for salmon.Figure 3. Lower Klamath River USGS water quality sampling stations. (source: USGS)Figure 4. Assisted Sediment Evacuation associated with the removal of Copco No. 1 Dam cofferdam on August 14, 2024. The mainstem Klamath flow is coming from bypass tunnel in upper center of photo. Figure 5. Timing of fall-run salmon return (daily counts) to the lower Shasta River weir-trap in years 2017-2020. (CDFW data)
A weekly survey by the US Fish and Wildlife Service1 targeting Delta smelt captured one Delta smelt in early August 2024 (Figure 1). It was the first and only Delta smelt caught this summer in that smelt-targeted survey in the Bay-Delta Estuary. A late April IEP juvenile fish survey (the 20-mm Survey) caught several juvenile Delta smelt in the same area (Figure 2).
What is unique about this location in Suisun Bay? In 2024 the low-salinity-zone (LSZ) has been located in Suisun Bay for most of the spring and summer, as Delta outflows have been maintained at 8,000-12,000 cfs (Figure 3). The LSZ is the critical spring-summer habitat of the Delta smelt (a salinity range related to high survival in the population). When the LSZ is in Suisun Bay, it generally remains within the maximum temperature tolerance of Delta smelt (70-72oF). When Delta outflow falls below about 7,000-8,000 cfs, the LSZ moves east into the warmer Delta. Delta water quality standards (D-1641) require a minimum outflow of 7,000 cfs in wetter years for this reason. When it is east in the Delta, the LSZ tends to have warmer water due to higher air temperatures. The Delta smelt biological opinions have a provision called “Fall X2” that requires extra Delta outflow in late summer to help ensure Delta smelt are west in Suisun Bay (Figure 4), where they have higher survival potential.
The LSZ does not occupy a large area – it is generally a small mixing zone where fresher water meets the saltier water. The LSZ moves up and down the estuary with the monthly and daily tidal cycles. The one smelt was caught in early August, when the LSZ happened to be at that net sampling location (Figure 5) because of the relatively high Delta outflows in summer of above-normal water year 2024. In contrast, much lower Delta outflows in summer of drought year 2022 brought saltier water to Suisun Bay (Figure 6), and the LSZ was upstream in the warmer lower Sacramento River channel of the Delta near Rio Vista (Figure 7).
In closing, there are a few Delta smelt left – but it is near the end of over five decades of population decline that has brought them single digits away from extinction (Figure 8). The cause in large part has been the devasting effects of low spring-summer Delta outflows in drier years that maintained the LSZ upstream of the Bay in the warmer Delta, where the smelt cannot survive. Efforts to protect the smelt in only in wetter years by requiring higher Delta outflows were positive, but requirements in wetter years alone are not enough: the smelt only live one year. The only option left is to maintain the 10,000-12,000 cfs Delta outflow in all years, raise the captured brood stock at UC Davis for release in the LSZ in the Bay, and hope the species can recover. The cost would be about 1 million acre-feet of water supply in the drier years over the summer.
The choice was made for us by DWR and in the soon-to-be-released US Fish and Wildlife Service updated biological opinion on the long-term effects of the state and federal water projects. The most recent opinion issued in 2019 stated the projects do not jeopardize the viability of the Delta smelt population. Now we seem intent on removing the one remaining lonely smelt. Just remember, the Delta smelt were supposed to be the “canary in the coal mine.”
Figure 1. The EDSM week-6 2024 survey results for Delta smelt. Note one smelt was captured in western Suisun Bay.Figure 2. The catch distribution of Delta smelt in Survey 4 2024 of the 20-mm survey. Figure 3. Delta outflow in summer 2024.Figure 4. Delta outflow in summer 2007-2024. Note above-normal water year 2024 had consistent summer flows of 8,000-12,000 cfs. Note wet years 2011, 2017, 2019, and 2023 had Fall X2, but 2024 has not.Figure 5. Salinity (ppt) and water temperature (F) in western Suisun Bay in summer of above-normal water year 2024.Figure 6. Salinity (ppt) and water temperature (F) in western Suisun Bay in summer of drought year 2022.Figure 7. Salinity (ppt) and water temperature (F) in lower Sacramento River channel of western Delta in summer of drought year 2022.Figure 8. Relationship (log-log) of the fall index to the prior summer index for Delta Smelt. Dry year production (red years) generally is an order of magnitude lower than wet (blue) and normal (green) water years from summer to fall (A vs C-D). The population declined based on both indices by over 99% from the 1970’s to the mid-2010’s. Note 1990 and 1991 had relatively high summer and fall indices because South Delta export rates were very low in the fourth and fifth years of drought because reservoir water storage was minimal. Note 2014 and 2015 had lower than expected fall indices under summer TUCP outflows. Water year 2017 (bold #17) was the initial year of the virtual extinction period for Delta Smelt observed in the Fall Midwater Trawl Survey.
Enhanced Delta Smelt Monitoring, 2024 Phase 3 Preliminary Analysis, U.S. Fish and Wildlife Service, August 30, 2024 DRAFT ↩
