Category Archives: Steelhead

A Report from Puget Sound

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Colleagues in the state of Washington write me (in italics below):

Sad to say but the Wild Fish Conservancy teaming with WDFW, using the ESA as a crutch, have eliminated pretty much all of the winter and summer steelhead fishing in Puget Sound streams. The salmon fishing regs are a mess and at the rate they are going, salmon seasons in Puget S. will vanish.

Comment: The salmon season was closed this year here in California to protect future fisheries. Puget Sound fisheries are closed to protect vanishing endangered breeds including Orcas1. Our hope here is that we protect both future fisheries and endangered species. One does not have to preclude the other.

With the massive human population increase in Puget Sound coupled with the anti-hatchery people, coupled with the inability of “habitat improvements” keeping up with habitat destruction, coupled with wildfires, climate change, low river flows/high water temperatures/extraneous bad water quality, things don’t look good for the future. ESA is only used here to eliminate hatcheries. Eventually, it will be just like the Redfish Lake situation where they got down to one returning male and had to go back to hatchery production. The ESU for Puget Sound includes all of the streams plus hatcheries. It seems that with the elimination of hatcheries, the anti’s will eliminate both the commercial and sport fisheries. What is really sad is the 36000 adult Chinook that were “surplus’ last year at the George Adams Hatchery and given to the crab fishermen (according to WDFW). The old WDFW people would have supported the anglers and tried to make things better. The current downward trend is near bottom (i.e., Chinook in Puget Sound declared extinct.)

Comment: It did not have to go this way in Puget Sound. It does not have to in California, either. We in California should learn from the mistakes to the north. There is a different way. More on the “way” in future posts.

Yuba River – Plan for New Fish Facilities at Daguerre Point Dam

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On May 16, 2023, the California Department of Fish and Wildlife, National Marine Fisheries Service, and Yuba Water Agency announced a plan to design and build a fish bypass at Daguerre Point Dam on the lower Yuba River (see Figure below).

At present, the dam has fish ladders on both ends of the dam that don’t work well.  The plan’s conceptual design is for a bypass channel that would allow fish to circumvent the existing dam; the plan would retain the dam.  The plan would reconfigure the diversion works at the dam’s south end and add effective fish screens to the agricultural diversion infrastructure at both ends of the dam.

Essentially, the bypass would operate as a long, high-capacity fish ladder that would also allow passage of sturgeon and lamprey, which cannot use the existing fish ladders.  In addition to improving the upstream migration of adult fish, the bypass would also allow for more natural downstream passage of juvenile fish.

For adult salmon and steelhead migrants headed upstream to spawn in the higher-flow, cooler, and gravel-abundant 10-mile reach between Daguerre Point Dam and Englebright Dam, the bypass would likely reduce delays caused by reluctance to enter the existing ladders and by the difficult ascent up those ladders.  For juveniles outmigrating downstream, the bypass could offer more natural conditions than simply spilling over the dam or seeking out the openings to the two ladders and passing downstream in the ladders.  The existing features place the young fish at the mercy of native and non-native fish predators below the dam.

The bypass concept is one of several designs that could reduce existing problems at Daguerre.  In addition to passage improvement, the concept could accommodate fish collection and segregation, and may be a feasible location for a conservation hatchery.

Several key elements should be added to this bypass plan, including:

  1. A segregation weir that that allows selective passage and capture of upstream and downstream migrants for processing and transfer.
  2. Predator removal, either at the segregation weir or by means of another nearby arrangement, to minimize predation below the dam. Predator control would likely benefit the entire lower Yuba system.  Major predators in terms of numbers and threat below Daguerre Dam include striped bass, smallmouth bass, pikeminnow, and American shad.
  3. Stream habitat improvements upstream, in the bypass, and below the dam, in particular those that create refugia for juvenile salmon, steelhead, and sturgeon, and that are less favorable to the fish that eat them.
  4. Fish handling, processing, and holding facilities.
  5. A conservation hatchery for salmon and steelhead.

Alternative designs should also be fully evaluated through CEQA/NEPA and CESA/ESA processes.  For example, one alternative may involve upgrading one or both of the existing ladders to include as many of the advantageous features as possible.

 

Radio-Tracking Study Greatly Advances Central Valley Salmon Science

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Over the past five years (2018-2022), federal and state biologists have undertaken a comprehensive study of salmon smolt migrations down the 350 miles of the Sacramento River from below Shasta Dam to the Delta, Bay, and ocean.  The study released thousands of radio-tagged late-fall-, spring-, fall-, and winter-run hatchery and wild smolts in the Sacramento River near Redding (RM 290), then tracked their progress and survival as they proceeded to Butte City (RM 170), the Tower Bridge in Sacramento (RM 60), and Benicia Bridge at the head of San Francisco Bay.  Each release group provides a story that is helping our understanding of salmon science in the Central Valley.  Most important are lessons learned about drought and climate change.  Much has been learned, with more to come.

An Example: Releases of Radio-Tagged Winter-Run Smolts

Radio-tagged winter-run salmon smolts from the federal Livingston Stone Fish Hatchery were released to the Sacramento River at Redding in winter of years 2018-2022.  Their signals were detected from Butte City to the Benicia Bridge at the head of San Francisco Bay.  For example, Figures 1 and 2 show detections from a release at Redding on 2/14/2019 of 650 radio-tagged smolts.  Figure 1 shows detections over the winter and early spring at Butte City, 120 river miles downstream of Redding.  Figure 2 shows detections at the Tower Bridge in Sacramento, 230 river miles below Redding.

Preliminary Findings

A summary of release-group survival in Table 1 indicates the following:

  • Survival was significantly compromised in dry years 2018, 2020, 2021, and 2022 compared to wet year 2019.
  • Survival was poor in the upper river and the Delta.
  • December late-fall-run releases during wet periods in generally dry years had relatively high survival.

Other findings include:

  • Smolts that received thiamine “boosts” in the hatchery had slightly higher survival.
  • Approximately 20-25% of smolts are diverted into the central Delta at Georgianna Slough
  • Survival among release groups within a year was often related to flow and/or water temperature after release (Figures 3 and 4).
  • Fall-run salmon grown in 2020-2021 at the Coleman Fish Hatchery on Battle Creek had significantly higher survival when released at Butte City than when released directly from the hatchery about 80 miles upstream of Butte City.

 

Table 1.  Percent survival summary for release groups by run and year.

Winter Run Hatchery Chinook – released at Redding

Year To Butte City To Sacramento To Bay
2018 18.4
2019 64.5 23.3 25.6
2020 25.8 13.2 3.5
2021 25.8 10.1 3.6

Late Fall Run Hatchery Chinook – released at Battle Creek Hatchery

Year To Butte City To Sacramento To Bay
2018 0.17
2019 23.5 4.8
2020 76.1 60.4 16.9
2021 36.6 14.3 4.7
2022 75.5 17.1

Battle Creek Hatchery fall run – released at Battle Creek Hatchery

Year To Butte City To Sacramento To Bay
2019 46.0 22.0
2020 36.4 9.1 0.1
2021 0.3 0.0

Battle Creek Hatchery fall run – paired study

Year To Sacramento To Bay
2021 at Battle Ck 1.7 0.0
2021 at Butte City 26.3 4.7

Feather Hatchery spring run – released in lower Feather River

Year To Sacramento To Bay
2019 49.4 26.2
2020 26.8 2.6
2021 28.6 2.2

Wild Chinook Red Bluff Release

Year To Butte City To Sacramento To Bay
2018 3.2
2021 2.2 0.0 0.0

American River Hatchery Chinook – lower American River release

Year To Sacramento To Bay
2018 68.1 2.0

Butte Creek Wild Spring Run – lower Butte Ck

Year To Sacramento To Bay
2018 27.2
2019 16.3 1.5
2021 0.0 0.0

Battle Creek Start-up Hatchery Winter Run Chinook to Battle Creek

Year To Butte City To Sacramento To Bay
2019 23.3 14.0
2020 17.5 9.4 0.0
2021 11.5 3.3 0.2

Figure 1. Detections at Butte City of hatchery winter run smolts released at Redding with flow at Butte City gage 2/14/2019.

Figure 2. Detections at Tower Bridge in Sacramento of hatchery winter run smolts released at Redding with lower Sacramento River flow at Wilkins Slough 2/14/2019.

Figure 3. Survival rate to Sacramento of wild Butte Creek spring run radio-tagged release groups with Butte Slough flow in 2018.

Figure 4. Survival rate to Sacramento of wild Sacramento River fall run radio-tagged smolts, Red Bluff release groups with lower Sacramento River flow and water temperature at Wilkins Slough in 2018.

American River Water Forum 2.0 – The Future for American River Salmon and Steelhead

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Conditions in the lower American River have been bad all year, and are getting worse.1 Folsom Reservoir storage never recovered this spring and is critically low this summer (Figure 1). Releases from reservoir to the river have been low (Figure 2), resulting in excessively warm river water temperatures (Figure 3).

In a recent post on the Water Forum’s blog, Jessica Law, the new executive director of the American River Water Forum, described current conditions for the lower American River:

I won’t sugarcoat it. Conditions in the river will be bad. However, the Water Forum and our partners are working hard to ensure conditions are as good as they can possibly be, and to minimize harm to fish and habitat. As you may have seen on the news, we began this year with a near-normal snowpack. In most years, the snowpack melts and feeds our lakes and rivers. This year, the snowpack disappeared in the span of several weeks, soaking into the dry soil or evaporating—perhaps foreshadowing what may turn out to be the case study for climate change impacts on our water supplies and environment.

In a recent interview with Matt Weiser posted in Maven’s Notebook, Ms. Law further elaborated about the update of the original Water Forum Agreement from the year 2000.

“The biggest thing we’ve done is develop and implement a Modified Flow Management Standard with Reclamation that governs water movement in the Lower American River and optimizes conditions for fish. So that’s huge. …

But at some point, nature is moving faster than we can keep up. This year, with another extreme drought in play, is a great example of that. We had better water storage in all reservoirs coming out of a dry year than we ever had. This was very intentional by Reclamation and the Department of Water Resources. Still, we’re in a really bad situation this year.

Yet there is more to the story than natural conditions. Notwithstanding the Modified Flow Management Standard, fisheries in the lower American River have been struggling for many years.2

Reservoir inflows are low and water temperatures are high in summer of drier years (Figures 3 and 4), because Reclamation fails to conserve storage and the reservoir’s cold-water pool in most years. In the drier years, high June releases to meet Delta requirements and/or export demands lead to lower summer storage and high July water temperatures (Figures 1-3). Low reservoir storage levels lead to lack of access to the cold-water pool. Peaking power releases in afternoon-evening period draw warmer water from the surface of the reservoir (Figure 5).

A part of the solution to the problem is to have strict rules on end-of-year storage (Figure 7):

  1. 500,000 AF in high-storage years
  2. 350,000 AF in intermediate-storage years
  3. 250,000 AF in low-storage years

It is no longer enough to set end-of-September storage targets. Climate change means in part that more autumn months are very dry. Exports in the fall (and a transfer season now extended through November) pull down CVP storage or at least slow reservoir refill. Storage at the end of November or end of December needs to an explicit part of the carryover calculus. Figure 7 shows end-of-November as the requirement.

Complying with these rules (criteria) would occur through strict management of summer-fall storage releases. It would begin with the higher requirements for high-storage years, when there is water to manage. This would help prevent excessive drawdown from cascading into catastrophic conditions in one year.

Conserving storage in spring of drier years is also important in maximizing water storage for the beginning of summer. Use of Folsom Reservoir to meet short-term Delta water quality demands in winter and spring of drier years like 2021 (Figure 6) exacerbates summer storage and water temperature problems. This also wreaks havoc on the lower American River’s steelhead spawning habitat and salmon and steelhead rearing habitat.3

What is running away from managers of the lower American River is not only climate conditions. It is also the relentless pressure on other Central Valley Project (CVP) and State Water Project (SWP) reservoirs that forces Folsom Reservoir to shoulder more of the burden than it can bear. The explicit goal of “maximizing deliveries” in purpose-and-need statements of the 2019 Biological Opinions for the operation of the CVP and SWP are just one aspect of this pressure.

The over-delivery of irrigation water from Shasta Reservoir to Sacramento River Settlement Contractors in the spring and summer of 2021 made much less water from Shasta available to meet Delta water quality needs. Hence, the sudden demands on Folsom. There is a direct line between deliveries along the Sacramento and the amount of water in storage at Folsom Reservoir. These related problems must be solved to allow implementation of Folsom storage levels to be truly protective.

In summary, Water Forum 2.0 should focus on conserving Folsom Reservoir’s cold-water pool, providing access to the cold-water pool, minimizing the adverse effects of peaking power on river water temperature, and minimizing use of Folsom storage for short-term Delta water needs. While much of the focus must be on drier years, especially years like 2015 and 2021, overuse in high-storage type years can also lead to future problems.

For more detail on the salmonids and their habitat conditions in the lower American River see https://www.calfish.org/Portals/2/Programs/CentralValley/LAR_RST/docs/2020%20LAR%20RST%20Emigration%20Monitoring.pdf .

Figure 1. Folsom Reservoir storage patterns in four drier years: 2001, 2008, 2015, and 2021.

Figure 2. Folsom/Nimbus Reservoir releases to the American River at Fair Oaks in June-July of four drier years: 2001, 2008, 2015, and 2021.

Figure 3. Water temperature in the lower American River at William Pond gage in June-July of four drier years: 2001, 2008, 2015, and 2021. Red line is the upper limit of water temperature considered safe for salmonids.

Figure 4. Dry years 2001, 2015, and 2021 June-July inflow to Folsom Reservoir. Note 2015 and 2021 were very similar.

Figure 5. 48 hours of flow (cfs/100) and water temperature (oF) from Folsom Dam beginning 7/26/21 at 08:00 hours.

Figure 6. Folsom Reservoir daily-average storage releases (cfs) October 2020 to July 2021. Note each rectangle represents approximately 15,000 acre-ft of storage water. The three peaks in spring represent approximately 100,000 acre-ft of the end-of-June storage in Figure 1, or roughly about half the difference between 2015 and 2021 beginning-of-the-summer storage. Higher releases at the end of 2020 also contributed to the difference, along with low precipitation and snowmelt in 2021.

Figure 7. Folsom Reservoir daily-average storage (acre-feet) 2000-2021. Recommended minimum storage criteria are shown by circles: blue for high-storage years; light blue for intermediate-storage years; yellow for low-storage years. Red arrows are years that grossly exceeded such criteria.

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.