Category Archives: Restoration

Flood Bypasses are Key to the Future of Wild Salmon in Sacramento River Valley Initial success of the Fremont Weir Big Notch

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The Big-Notch Project at the Fremont Weir came online in late 2025. In this post, I describe events in December 2025 that provided improved access for juvenile salmon to floodplain habitat in the Yolo Bypass through that new Big Notch.

The goal of notch projects at the Fremont and Tisdale weirs in the Sacramento Valley is to create greater access to floodplain habitats for juvenile winter-run Chinook salmon, as well as fall-run and spring-run, in the upper Sacramento River Valley. The Fremont Weir project, completed in 2025, now improves access for salmon into the Yolo Bypass. The Tisdale Weir notch project, when completed, will improve access of upper Valley salmon populations into the Butte Basin and the Sutter Bypass floodplains.

Background on Floodplains and Butte Creek

The recovery and success of Sacramento River winter-run Chinook salmon is tied to floodplain rearing and smolt production in the wettest years. There is great potential improvement for the survival of endangered winter-run salmon by providing improved rearing access to the Sutter and Yolo flood bypasses.

The remarkable recovery of Butte Creek’s wild spring-run Chinook salmon at the turn of the 21st Century provides an excellent example.

The turnaround in Butte Creek followed a decade of restoration activity in the creek and its floodplain by the US Fish & Wildlife Service, the California Waterfowl Association, the Nature Conservancy, CalTrout, Friends of Butte Creek, duck clubs, rice farmers, and many other collaborators.1 The secret to the success was opening the Butte Basin and Sutter Bypass so that juvenile salmon could rear in the floodplain habitat in early winter. This led to accelerated growth and high survival, which in turn allowed early entry of smolts into the ocean by late winter and early spring.

How the Fremont Weir Big-Notch Project Worked in its First Year

The first significant winter rains of 2025 brought a strong pulse of flow to the lower Sacramento River in late December (Figure 1). That pulse began entering the Big Notch at the Fremont Weir on December 21st (Figure 2). River flow (and flow exiting the Sutter Bypass) passed through the Big Notch through the end of December. River flow was only high enough to overflow the entire Fremont Weir on Dec 27 and 28 (Figure 3). Thus, most of the water flowing into the Bypass at the Fremont Weir passed through the Big Notch. Lesser but substantial amounts of warmer water also flowed into the north Yolo Bypass via the Knights Landing Ridge Cut (Figure 4).

Overflows into the Yolo Bypass (also including the Sacramento Weir) rapidly fill the Bypass (see maps). The Bypass floods to depths of 8-10 feet (Figure 5). The slowing of flows and spread of shallow water leads to rapid warming (of the colder river water) in the flooded Bypass (Figure 6). The warming extends to the lower Sacramento River channel in the north Delta at the Rio Vista Bridge (Figure 7), downstream of the Yolo Bypass’s outlet.

The warmer shallow Bypass habitats (optimal growth 52-56ºF) have high food production that supports increased growth and survival of juvenile winter-run emigrating to the ocean. Substantial numbers of juvenile winter-run salmon likely entered the Yolo Bypass during the December event through the new Big Notch (Figures 8 and 9).  The access to the floodplain habitat likely contributed to the higher winter-run smolt 2025 index of the winter-run Juvenile Production Estimate (JPE, Figure 10) and the annual Chipps Island Trawl Survey index (Figure 11). Winter overflows into the other flood bypasses and the relatively wet water year 2025 also contributed.

The Benefits of Notches in Flood Bypass Weirs

The principal benefits of weir notches are that they allow water to enter flood bypasses (overflows) at lower river stages (at stages up to 10 feet or lower), and thus earlier in the late fall or winter. These systems can also enable overflow events during dry winter seasons that would not typically experience overflows. They also allow overflows later in the winter season to enhance adult and juvenile migrations of all the salmon runs through the bypasses (Figures 12 and 13).

The notches can also sustain overflows between periods of normal weir overflows. This not only sustains the access, but also reduces potential for stranding of adult and juvenile salmon. It also maintains good habitat conditions, minimizing overheating or disconnection of bypass habitats.

The broader overall benefits of weir notches are improved smolt production to the ocean, greater sustainable ocean harvest, and improved spawner numbers (escapement).

Map of Sacramento River Valley with Flood Weirs and Bypasses.

Map of Yolo Bypass – (Note fishery monitoring program sites.)

Map of Colusa Basin Drain and Yolo Bypass Tule Canal flow pathway to Rio Vista Bridge.

Figure 1. Streamflow in the lower Sacramento River below Wilkins Slough in December 2025. Source: CDEC.

Figure 2, Streamflow in the Yolo Bypass downstream of the Big Notch in the Fremont Weir.in December 2025. Source: CDEC.

Figure 3. Overflow into the Yolo Bypass at the historical Fremont Weir in December 2025. Source: CDEC.


Figure 4. Streamflow in the Ridge Cut Slough (Colusa Basin Drain connection to the upper Yolo Bypass below the Fremont Weir in December 2025.

Figure 5. Stage in the Tule Canal of the Yolo Bypass at Lisbon gage in December 2025.

Figure 6. Water temperature at the Lisbon gage in the Yolo Bypass in December 2025.

Figure 7. Daily average air and water temperature and river stage at the Rio Vista Bridge of the Sacramento River channel of the north Delta in December 2025. Source: CDEC.

Figure 8. Daily catch of older salmon (non-fry, predominantly winter-run) in Tisdale Screw Trap and environmental conditions September 2025 to May 2026.

Figure 9. Daily catch of older salmon (non-fry, predominantly winter-run) in Sacramento River near Sacramento beach seines and environmental conditions September 2025 to May 2026.

Figure 10. Juvenile Production Estimate (JPE) of winter-run salmon entering the Delta by brood year.

Figure 11. Cumulative catch index of winter-run salmon in Chipp Island Trawl Survey In the east Bay by brood year.

Figure 12. Fry of spring-run and fall-run salmon would enter the Big Notch of the Fremont Weir under these conditions in January-February 2026. The Wilkins Slough flow of the Sacramento River of <30,000cfs indicates most of the flow that would enter the Bypass would be via the Big Notch. Note: Some flow at the Big Notch entrance would also come from the exit of the Sutter Bypass.

Figure 13. Flow (cfs) in the northern Yolo Bypass in winter 2026. Most of the flow came from the Big Notch. Bypass water temperatures (not shown) were best for salmon fry at 50-55ºF in the January period but reached stressful levels >65ºF in the March period.

Klamath Dam Removal is Complete – How well did it go?

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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)
  1. See Facebook (Klamath River & Dam Removals) ↩

Klamath Dam Removal Update – April 6, 2024

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Video Screen Grab of lower Jenny Creek ASSISTED SEDIMENT EVACUATION PROJECT

In a March 20 post, I related events in the Jan-Feb 2024 period of the Klamath Dam Removal Project.  The initial four-reservoir drawdown in January led to abrupt increases in streamflow, suspended sediment, and low dissolved oxygen levels above and below Iron Gate Reservoir (the lower reservoir).  This was followed by lower stable streamflow, high dissolved oxygen, and declining suspended sediment.  Streamflow pulses from upstream Klamath Lake in late February and early March resulted in (short-term) elevated suspended sediment from exposed sediment erosion in the four reservoir reaches.  These circumstances were expected as part of the four Dam Removal Project.

In March, the Assisted Sediment Evacuation Project began in the Jenny Creek floodplain of the Iron Gate Reservoir footprint.   That project has led to lethal doses of suspended sediment (turbidity) in the lower Klamath River below the Iron Gate Dam site (Figures 1-3).  Project approvals, such as the National Marine Fisheries Service’s (NMFS) biological opinion quoted below, included provisions to stabilize sediments after the January drawdown, but not to flush sediments into creeks and the Klamath River.

Post drawdown and dam removal, crews will be working to actively restore the exposed reservoir footprints and tributary mouths that flow into the former reservoirs. To reduce elevated suspended sediment concentrations (SSCs), the Renewal Corporation will take active measures to flush sediment from the reservoirs during drawdown and then immediately begin stabilizing remaining sediment after drawdown has been completed. Revegetation, channel construction, and placement of habitat features such as logs and boulders will minimize erosion and allow passable channels to form in preparation of fish presence. (NMFS Biological Opinion p. 14)

The origin of the high suspended sediment levels was likely from the exposed bed of Iron Gate Reservoir (particularly the Jenny Creek arm), not upstream reservoir erosion during the Klamath Lake flow pulses.  Sediment levels below Iron Gate Dam were low during the flow pulse that diluted the high sediment loads from Iron Gate Reservoir (Figure 1).  Gages below Copco and JC Boyle reservoirs were lower, generally below lethal levels (Figure 4).

Chinook salmon fry are abundant and most prevalent in the lower Klamath River below Iron Gate Dam in late winter (February-March).  Coho and steelhead fry are more abundant later during spring.

The Assisted Sediment Evacuation Project is slated to end on April 15.  I recommend that it cease immediately, with efforts shifted to “stabilizing remaining sediment,” in order to minimize impacts of the project on Klamath River salmon and steelhead.

Figure 1. Turbidity and streamflow in the Klamath River below Iron Gate Dam (rm 193) in January to March 2024. Note turbidity of 300-500 SBU is roughly 1000-2000 mg/l total suspended sediment (TSS). Such levels are considered lethal for juvenile salmon and steelhead.

Figure 2. Turbidity and streamflow in the Klamath River near Seiad Valley below the mouth of the Scott River (rm 145) in March 2024.

Figure 3. Turbidity and streamflow in the Klamath River near Seiad Valley about ten miles upstream from the mouth of the Scott River (rm 145) in March 2024.

Figure 4. Turbidity and streamflow in the Klamath River just upstream of Iron Gate Reservoir and below Copco dams in March 2024.

Mormon Crickets and Pikeminnow

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When settlers moved into the desert west a century or so ago and started irrigating crops, they created new habitats for some species that Mother Nature had held in check. Species such as Mormon Crickets became pests, overwhelming the irrigated crops produced in the unnatural habitats and plaguing their human guests.1

The same goes for the Sacramento pikeminnow. The dams and farmland reclaimed from wetlands in California’s Central Valley have created ideal habitat for the pikeminnow. Pikeminnownow have become so abundant they have become predator nuisances that feed on ever-decreasing numbers of young salmon and steelhead. Pikeminnow also migrate from the Delta to spawn in valley rivers below dams where they prey on young salmonids. Juvenile pikeminnow compete with young salmonids for aquatic insects and feeding territory.

The problem also occurs on the Eel River, a large coastal salmon river that once featured some of the largest salmon and steelhead runs in California.2 Sacramento pikeminnow are not indigenous to the Eel River: they were introduced by anglers who brought “minnows” to use as bait to fish for trout stocked in PG&E’s Lake Pillsbury on the Eel River’s mainstem.

There are three ways to deal with the pikeminnow problem. One is to selectively eradicate them. The Columbia River water folks tried this first approach for decades now – that has not worked.3 The Eel River folks are trying weir traps.4

Another approach is to reduce the habitat conditions that allowed enables the high production of pikeminnow in the first place. Replacing warm, slow-moving pools with colder, faster-moving water makes habitat less conducive to pikeminnow.

A third approach is allowing salmon and steelhead to get to places the pikeminnow are not. Many organizations are seeking the removal of Scott Dam, which creates Lake Pillsbury. This will allow salmon and steelhead access to the Eel River upstream of the current lake. There are natural barriers upstream that steelhead and salmon can pass but that pikeminnow, which are weaker swimmers, cannot.

To help recover our native salmonids in the Central Valley, a combination of weirs and colder water, reverse engineering the habitat to reduce pikeminnow production, and the reintroduction of salmonids in higher elevations too cold for pikeminnow could be the recipe for success.

Cache Slough Tidal Wetland Restoration – Update More misguided resource-damaging habitat restoration for an already highly altered and compromised Delta

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Cache Slough Complex Restoration

The Cache Slough Complex is in the lower (southern) Yolo Bypass in the north Delta region (Figure 1). It is the focus of the state’s tidal wetland restoration EcoRestore Program that spans 16,000 acres in the Cache Slough region of the Sacramento-San Joaquin Delta.

The 53,000-acre Cache Slough Complex is located in the northwest corner of the Sacramento-San Joaquin River Delta in Solano and Yolo counties (Figure 1). The Yolo Bypass receives inflow directly from the Sacramento River (Fremont Weir), the Colusa Basin Drain, Putah and Cache creeks, and agricultural and municipal discharges. The Cache Slough Complex exits the Yolo Bypass via Cache Slough, first connecting to the outlets of Miner and Steamboat Sloughs, before entering the tidal Sacramento River channel near Rio Vista.

The Cache Slough Complex has been identified as an area with great potential for tidal restoration as a result of its connectivity with the Yolo Bypass floodplain, suitable elevations, high turbidity, high primary and secondary productivity, and use by Delta smelt (Hypomesus transpacificus), Chinook salmon (Oncorhynchus tshawytscha), and other native fishes. Both federal and state wildlife agencies consider the Cache Slough Complex to be a prime area to advance habitat conservation to benefit endangered species in the Sacramento-San Joaquin Delta and incorporate improvements to the regional flood management system.

The latest project approved for construction is the Lookout Slough Project, a 3000-acre tidal marsh restoration immediately to the west of Liberty Island. The Project was certified by DWR in 2020 as mitigation/compensation for the Delta Tunnel Project. The Delta Stewardship Council recently denied appeals1 to the state’s certification of the Lookout Slough tidal marsh restoration project. Once completed, Lookout Slough will be the Delta’s largest single tidal habitat restoration project to date.

The Problem

Most of the tidal “restoration projects” in the Cache Slough Complex involve breeching leveed tracts of agricultural land to create subtidal or intertidal habitat. Tidal waters once confined to narrow floodplain channel are now allowed to pour through breaches onto over 10,000 acres of formerly diked farmlands. The process started between 1980 and 2000 when Little Holland Tract (1456 acres) and Liberty Island (4340 acres) levees failed and were not repaired, leaving these lands open to the tides. Because these reclaimed wetlands had subsided during active farming, most of the “restored tidelands” became sub-tidal, year-round, warm, shallow, open-water habitat. Such habitat is too warm for Delta native fishes except during the winter.

The enhanced tidal exchange and warm productive winter and early-spring habitat attracts migratory Delta native fishes like smelt, splittail, and salmon to the Cache Slough Complex. While such habitat is considered beneficial in winter, it warms excessively in spring and summer, reducing the period of quality rearing, and can reduce overall survival and production. Native fishes have succumbed to the heat, stranding in the uneven landforms, and predation by non-native warm-water fish.

The latest projects, Lower Yolo Ranch (1749 acres), Yolo Flyway Farms (300 acres), and Lookout Slough (3000 acres), will add 5000 acres of mostly shallow intertidal habitat. Tidewater will flood onto these lands twice a day to warm in the California sun and then return to cooler deep, shaded, sub-tidal sloughs long considered prime Delta smelt and salmon rearing habitat. Not only will the new inter-tidal “wetlands” be too warm, but they will contribute to warming adjacent sub-tidal sloughs that convey water to and from other parts of the north Delta. This water quality degradation gets worse with each new project and has resulted in the degradation of the entire north Delta as a viable spawning, rearing, and critical habitat of Delta smelt. The effect has measurably contributed to the near extinction of Delta smelt.

The Evidence

The United States Geological Service has many water quality and flow monitoring gages in the Cache Slough Complex (Figure 2) that provide considerable evidence of the above-described problem. Specific gages with pertinent data records reviewed for this post are highlighted in Figure 2.

Waters in the northern Cache Slough Complex become too warm for salmon and smelt (>20ºC) by spring (Figure 3). In summer (Figure 4), water tidally flooded into subtidal island-tracts can warm 5-7ºC over a day before draining back into adjacent sloughs. Water temperatures in the northern sloughs of the Cache Slough Complex reach 25ºC (lethal to smelt) or higher in summer, even in wet and normal water years (2016-2018, Figure 5). Water temperatures in the southern Cache Slough Complex are only slightly lower (Figure 6). Over the past decade, water temperatures in the Cache Slough Complex overall have been gradually increasing (Figures 7 and 8), to the detriment of Delta native fishes.

The Solution

The problem can be lessened or even reversed at existing and future restoration projects by:

  1. Limiting tidal access to sub-tidal sites to winter, when water and air temperatures are colder.
  2. Building projects with flow-through tidal channel features rather than a single opening.
  3. Ensuring that projects are inter-tidal with small, narrow, shaded channels, or tule benches.
  4. Narrowing, deepening, and shading connecting tidal sloughs.
  5. Limiting discharge of warm agricultural wastewater into tidal channels.
  6. Providing supplementary inflow of Sacramento River water from the Fremont Weir, from the entrance gates of the Sacramento Deepwater Shipping Channel, or from other locations.
  7. Retrofitting existing restoration sites and designing future projects as outlined above.

 

Figure 2. USGS gage locations in the Cache Slough Complex.

Figure 3. Water temperatures recorded at Little Holland Tract in 2015-16.

Figure 4. Water temperatures and water surface elevation (gage height) recorded at Little Holland Tract in July 2017. Note higher water temperature spikes occurred with strongest ebb (draining) tides.

Figure 5. Water temperature in Liberty Cut adjacent to Little Holland Tract, 2016-18.

Figure 6. Water temperature and tidally-filtered flow rate in Sacramento Deepwater Ship Channel, April-September 2021.

Figure 7. Water temperature in lower Cache Slough, 2011-2016.

Figure 8. Water temperature in the lower Sacramento River channel near Rio Vista, 2010-2019.