Category Archives: Steelhead

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.

State Water Board to Decide Fate of Shasta and Scott River Salmon and Steelhead – Part 2, the Scott River

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On July 1, 2021, staff from the State Water Resources Control Board (State Board) held a public Zoom meeting to provide information and solicit input on potential actions that could be implemented to address low flows in the Scott River and Shasta River watersheds (Figure 1) during the ongoing drought.  The Scott and Shasta rivers are major salmon and steelhead producing tributaries of the Klamath River. The State Board’s July 1 workshop sought input and options prior to taking action.   

 CSPA is providing comments through this three-part series.  Part 1 was the introduction, with a description of the general problems and solutions.  This is Part 2, with specific comments on the Scott River.  Part 3 will cover the Shasta River.

The Scott River Problem

The Scott River has a chronic low streamflow problem that occurs in the summer and fall of most years.  Only in very wet years, do ranchers and fish for the most part get the water they need.  In most years, nearly all the water in the watershed goes to agriculture, while the lower river and its tributaries run virtually dry.  Fish survive in the upper reaches of the river and in the lower tributaries that receive snowmelt and spring water from the adjacent Marble and Trinity mountains.  There are also spring-fed refugia in the middle sections of the river and In tributaries to the lower sections of the river.  But at many locations in the watershed, a large portion of the surface-water flow goes underground into near-surface aquifers, only to resurface as springs and be further diverted or extracted by wells, or go back underground.

The California Department of Fish and Wildlife is recommending summer minimum flows from 30-50 cfs at the lower end of the river to protect over-summering juvenile Chinook and Coho salmon, and steelhead.  These recommended flows represent roughly half of the available summer baseflow water supply in the Scott River.  Without a minimum flow requirement, almost the entire summer baseflow is  consumed by a carefully distributed water supply extraction system regulated by seniority-based surface water rights and overseen by the State Board or by minimally regulated groundwater pumping.  A large portion of the consumption occurs by means of minimally regulated shallow well pumping from the valley’s alluvial floodplain aquifer.  This supplies water for stock watering, pasture irrigation, or large scale sprinkler irrigation of hayfields.  The aquifer is recharged by surface flows and applied irrigation, and in places is augmented by beaver dam flooding.  The floodplain was once known as “beaver valley”.  However, much of such wetland floodplain habitat has been lost to channelization to enable irrigated agriculture.

There are many areas in the watershed that provide refugia for over-summering salmon and steelhead.  The extent of these refugia decreases over the summer as the surface water supply declines and springs cease flowing.  The loss of refuge habitat over the summer is greatest in drought years.  As the extent of refuge habitat declines, juvenile salmon and steelhead become more concentrated or succumb to “catastrophic stranding” where they die from refugia drying up or overheating.  Many refugia are on private lands.  Many are unidentified.  They need to be identified and surveyed to determine their characteristics and need for protection.

Drying rivers also pose problems for emigrating juvenile and immigrating adult salmon and steelhead in the fall and winter.  When fall rains and winter snow are lacking or late, juvenile fish are hindered or blocked from moving downstream to the Klamath River.  Adult fish cannot move upstream to spawning grounds in the valleys.

General Solution Options for the Scott River

Other than CDFW’s recommended minimum instream flows to save the fish (which would be successful), there are further options to help the fish.  One major option is to protect through the summer-fall season the many refuge areas that are present and functioning at the end of the spring snowmelt season. This can be accomplished in several ways:  (1) not allowing any diversion of surface or groundwater within or near the designated refuge; (2) pumping well water directly into the refugia; (3) diverting other surface waters into the refugia; and (4) protecting and enhancing refuge habitat (e.g., cattle fencing, riparian plantings, channel improvements).  The basic concept is to protect and enhance cold-water habitats of the refugia.  Each refuge will have its own prescription.  Some may benefit from introduced beaver colonies.  Note that some landowners working with CDFW and local stakeholder groups have accomplished some of these actions at varying scales of effort and with varying degrees of success.

Another solution option is a program to scale back seasonal agricultural water use based on the needs of fish and their habitat, as well as those of the landowners.  For example, a major problem for Scott River salmon is not being able to ascend into Scott Valley in the fall because of low streamflows.  Unlike the Shasta River Watershed, in which irrigation is disallowed after October 1, irrigation is allowed into December in the Scott watershed.  Scott Valley hay-crop irrigators in particular could cease irrigating a month or two earlier, foregoing late season cuttings.  This option was suggested by a landowner of a large ranch who was even willing to use his large-capacity wells to help water the river during the fall salmon migration.

Specific Recommended Solutions

The following recommendations offer large potential benefits with limited impacts and costs.

1.      Focus on the surface water irrigation diversions – all should cease in summer of dry years

Two large diversions with large canal distribution systems make up the bulk of the surface water diversions in Scott Valley, at least in wetter years or spring of drier years.  If these have not as yet cut back diversions as in most dry years, their diversions should cease.  The largest diversion, Young’s Dam, is a relatively large concrete structure with a fish ladder (Figure 2).  In summer of dry years, it usually does not divert, but does back up water in the river channel, causing significant rises in water temperature.  More flow would minimize such heating.  More flow is necessary to provide upstream passage of adult salmon in late summer and fall through the dam’s fish ladder, even when the dam is not diverting water.

The second largest surface diversion is Farmers Ditch, which diverts directly from the Scott River channel (Figure 3).  It too usually does not divert in summer of dry years, due to lack of surface flow.  Prior to ceasing its diversions, it contributes to drying up the river in the downstream tailings reach.

There are many small diversions1 in the middle and upper valley from reaches of the river and lower tributaries that retain flows in the summer.  Locally, they divert significant portions of the available streamflow.  Some are crudely designed and operated, and are unregulated (Figure 4).  All surface diversions should cease operating, since most are from spring-fed stream reaches supporting rearing salmon and steelhead.  In many cases, such diversions contribute to the dewatering of downstream reaches.  One such example is lower Shackleford Creek, where multiple small diversions in flowing spring-fed sections in the several miles upstream contribute to the drying up of the creek near its mouth on the Scott River (Figure 5).

2.      Middle and lower reaches of Scott River affected by groundwater pumping – all well pumping from locations contributing to dewatering of the main channel of the Scott River or lower tributaries should cease pumping.

Most free-flowing reaches of the middle and lower Scott River and its lower tributaries are over-summering juvenile salmon and steelhead refugia.  Even warm low flows provide some cooler hyporheic flow to sustain young salmon and trout in microhabitat areas of the stream channel (Figure 6; also see videos referenced at the end of this post).  Such locations cannot support high population densities for long and thus could use added flow to sustain them.

3.      Refugia in middle and lower reaches of Scott River and lower tributaries affected by groundwater pumping could be supported by pumping cold groundwater into stream channels to help sustain refuge habitat.

In reaches where groundwater pumping is no longer needed, idle wells can pump cold groundwater directly into stream channels to sustain specific refugia or to provide added flow for fish migrations.  Many ponds situated within the Valley’s water table have cold water that could be drained or pumped to refuge areas.  The tailings reach in the upper end of the Valley has many such ponds.

Summary and Conclusions

All surface diversions from free-flowing reaches of the Scott River should cease in summer-fall of 2021.  All such reaches are fed by snowmelt or springs, and are most likely refugia for over-summer rearing salmon and steelhead.  All well pumping near the river and lower tributaries that may affect springs or hyporheic flow in refugia should be cut back to help sustain the refugia.  All refugia should be identified and classified to value and need.  Where feasible, wells or surface waters can supply supplemental water to sustain refugia.  All refugia should be mapped, surveyed, and characterized for need; high value  options should be identified and implemented.  All irrigation in the Scott Valley (not including stock watering) should cease by October 1, as is already done in the Shasta Valley.  Cutbacks of well pumping for Scott Valley irrigation should commence on a graded scale on August 1 and September 1.

Figure 1. The Scott River and Shasta River Valleys in northern California west of Yreka, CA (Yreka is located in the Shasta River Valley). The Scott and Shasta Rivers flow north into the Klamath River, which runs west to the ocean. The Salmon River watershed is immediately west of the Scott River watershed. The upper Trinity River watershed is immediately to the south of the Scott River watershed.

Figure 3. Farmers Ditch diversion located in upper middle valley on Scott River.

Figure 2. Young’s Dam and diversion located on the Scott River in mid-Valley.

Figure 4. An unnamed small diversion located in spring-fed reach of Scott River below tailings reach. Both the river and diversion ditch contained large numbers of juvenile coho salmon.

Figure 5. The mouth of Shackleford Creek on Scott River in late summer.

Figure 6. Reach of the lower Scott River upstream of Fort Jones near Eller Bridge, nearly dewatered by groundwater pumping and lowering of the groundwater table. Despite lack of flow, the reach retains some over-summering refuge pools sustained by groundwater and hyporheic flow. Eventually, these areas become too warm, and many thousands of juvenile salmon and steelhead die. Such areas would benefit from a cessation of irrigation with water sourced from adjacent wells. Idle wells could be employed to add cold water to sustain the refugia.

Available Videos of Scott River Refugia

 

 

 

  1. There are approximately 800 water right holders in the Scott River watershed. ↩

Water year 2021 is a bad year for American River wild salmon and steelhead production.

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Water year 2021 has been bad for American River salmon and steelhead, with very low Folsom Reservoir releases Oct-Jan (Figure 1a).  Water year 2021 can best be described as a dry year, at least through the first quarter, somewhat on the drier side of 2018 and 2020, which were below normal water years.  However, whereas 2018 and 2020 followed wet years, water year 2021 follows a drier year.  This means 2021 started with poorer Folsom Reservoir storage (Figure 1b).

Water year 2021’s low fall and early winter reservoir releases from Folsom were nearer to 1000 cfs than the normal 2000 cfs.  As a result, much of the good spawning and early rearing fry habitat in the river below the dams remained dry (Figure 2).  In contrast, even in drought year 2014, the side channel spawning habitat remained slightly watered at 600 cfs river flow (Figure 3).  So, not only are redds dewatering in early winter of these dry years, the dewatering or drying of the side channels is getting worse.  This is either because the main channel is incising from persistent scouring or because sediment deposition blocks the entrance to the side channels, leaving perched side channels high and dry.

What got us into this predicament?  Was it simply Mother Nature or global warming?  Water management should take part of the blame (Figures 4 and 5).  The end-of-September Folsom storage in 2019 was higher than average at 700 TAF after a wet year.  Flood control rules required reservoir levels to be down to 600 TAF in November.  But storage dropped to 500 TAF, with higher-than-normal fall releases (Figure 6), essentially shorting the reservoir 100 TAF in the new 2020 water year.

The American River Water Forum Agreement Is designed to manage and protect all water users, including salmon.  Its formula for reservoir releases is based on natural flow input levels to the reservoir for that water year, which was lower than normal in 2020, thus leading to the prescribed low fall 2020 reservoir releases.  With reduced storage and low reservoir inflow in 2020, it was impractical to release the needed 2000 cfs for salmon and steelhead in fall 2020 without dropping the reservoir down to 200 TAF in what could be a drought year.

In conclusion, the American River salmon and steelhead are at the mercy of a precarious water management system that can go from good to bad in one water year.  One answer to this low fall flow problem is to ensure there is an extra 50-100 TAF of reservoir storage at the end of September to maintain the needed higher fall and winter flows for salmon and steelhead.  Because the channel morphology also continues to change, sediment supply and river morphology must also be taken into account, if not also adjusted.

Figure 1. Oct-Jan Folsom Reservoir releases 2017-2021 with long term average (above) and reservoir storage (below).

Figure 2. Sunrise side channel (looking upstream) end of January 2021 with some of the best spawning and rearing habitat for salmon and steelhead in the lower American River nearly dry with river flows at 1000 cfs. Other important side and main channel spawning and rearing habitats were similarly compromised. Note main channel is at extreme left middle of photo.

Figure 3. Sunrise side channel (looking downstream) on January 15, 2014. Some of the best spawning and rearing habitat for salmon and steelhead in the lower American River is in this side channel. In 2014 as shown, it was almost dry with river flows at 600 cfs. Note tops of salmon redds sticking out of the water in various stages of dewatering. The redds were dug by salmon earlier in fall 2013 at 1200 cfs.

Figure 4. Folsom Reservoir storage (acre-ft) in fall 2017-2020. Water years 2017 and 2019 were wet years, and water years 2018 and 2020 were below normal years.

Figure 5. Folsom Reservoir releases (cfs) in fall 2017-2020. Water years 2017 and 2019 were wet years, and water years 2018 and 2020 were below normal years.

Figure 6. Folsom Reservoir release (cfs) in fall 2019 with 64-year average.

Central Valley Steelhead 2021

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The Delta Science Program plans to host a Steelhead Workshop on February 17 – 19, 2021.  The purpose of the workshop is to “identify challenges to managing and monitoring Central Valley steelhead with the goal of identifying collaborations that are needed to improve the monitoring and science network for the species in the San Joaquin basin.”  While commendable and needed, such a workshop could and should cover the entire Central Valley Evolutionary Significant Unit (ESU), all of which must pass through the Delta on the way to and from the Pacific Ocean.

Although Central Valley steelhead science and management can succinctly be described as a mess, there are a few basic facts and misconceptions worthy of note that are useful in considering steelhead management in the Central Valley.

First, the facts:

  1. Steelhead are rainbow trout that have the genetic inclination to spend some of their life cycle in the ocean. Most rainbow trout have such an inclination, but some populations have long ago given up on that inclination (g., redband rainbow trout).

  2. In the Central Valley, all rainbow trout residing in anadromous waters are considered steelhead and are thus protected unless their adipose fins are clipped, which definitively shows hatchery origin.

  3. Rainbow trout of a wide range of origin, stocked or wild, live in or above dams in the Valley and are not designated steelhead. Some are remnants of steelhead trapped behind dams.  Other were hatchery raised or perhaps are remnants of long-ago geologically isolated populations.  Many of these non-steelhead pass over or through the dams and mix with steelhead, essentially becoming steelhead and influencing steelhead population genetics.

  4. All steelhead populations in the Valley have some degree of domestication from more than 100 years of hatchery influence and manipulation. Hatcheries (federal, state, and private) continue to influence population genetics.  Valley hatcheries have brought in eggs from many sources (g., Columbia River, coastal stocks, interior stocks such as Kamloops rainbow trout).  Hatcheries manipulated many important natural traits through selective breeding (e.g., run timing, age of maturity, growth rate).  Such changes affected the genetic integrity of locally adapted populations, adapted traits gained over thousands of generations.  Some hatchery sources were selected for traits better suited for hatchery managers or anglers than for natural diversity and population endurance.

  5. Valley steelhead come in many different breeds and colors, with distinct characteristics, traits, behaviors, and appearance. The basic breeds are often described by run timing:  winter, spring, summer, and fall, although most spawn in winter or spring.  Some examples are shown in attached figures below.

  6. Natural selection continues to adjust to human influences, albeit in competition with hatchery domestication.

Some misconceptions:

  1. Hatcheries are managed for benefit of natural, wild, or native steelhead populations. No. Hatcheries are managed to meet mitigation smolt production quotas at minimal cost, with some consideration for angler preferences (e.g., trophy size).  Hatchery domestication effects on genetic integrity are severe and not lessening.

  2. Central Valley steelhead are not in danger of extinction. Wrong.  They are in danger, which is why they are state and federally listed, and why no wild (unmarked) rainbow trout can be harvested in the anadromous zone of the Central Valley.  Wild “native stocks” are rare and declining.

  3. Spawning and rearing habitat in rivers and dam tailwaters are maintained to protect wild steelhead.   Protective standards are inadequate or often unmet.  Natural spawning and rearing habitats are degraded and are further deteriorating or being lost.  Flows are too low, and water temperatures too high.

  4. Steelhead are compatible with introduced non-native sportfish. No.  Striped bass, black bass, catfish, sunfish, and American shad all prey upon steelhead – the total population effect is substantial.  Since predatory fish cannot be eradicated, the interaction between steelhead and predators needs to be managed.

  5. Climate change is the cause of declining natural populations. Though climate change is real and exacerbates harmful conditions for steelhead, blaming climate change for the decline of steelhead is just a convenient excuse.

Management needs:

  1. Improved monitoring of steelhead population dynamics is needed. Despite the angler-funded steelhead stamp program, there is minimal monitoring of adult spawners or juvenile  Screw traps are for migrating fry, but steelhead fry don’t migrate like salmon.

  2. River habitats should be restored and improved. Rivers should not be treated just as conduits from hatcheries to the ocean.  Steelhead over-summer at least one year before emigrating to the ocean.

  3. Mitigation hatcheries should be converted to conservation hatcheries. The hatchery programs need a cleansing.  Also, hatchery rainbows released above dams should be marked.

  4. Spawning habitat should be for wild, native steelhead. Steelhead sanctuaries are needed.  Every effort should be made (selective barriers) to limit access to these areas by hatchery or stray steelhead, and by migratory non-native predators and competitors such as shad and stripers.

  5. Flows are needed to increase survival of wild steelhead fry and smolts. Steelhead are genetically adapted to emigrate with the natural flow pulses of fall, winter, and spring.  Reservoirs have eliminated or reduced such flows.  Without the flows, smolts won’t migrate or survive the predator gauntlet.  Trap and hauling wild smolts around the lower river and Delta predator gauntlet is an option for dry years.

  6. Flows are needed to improve attraction of adult migrants to spawning rivers. Again, steelhead need the flow pulses.

For more on steelhead see:

Native rainbow-steelhead from the lower Yuba River. Many wild rainbow trout do not migrate, choosing to remain in the cold tailwaters of dams, where they sustain high-quality sport fisheries.

An early fall run hatchery steelhead from the lower American River in October. Battle Creek hatchery steelhead smolts were stocked in the American River for one year to determine if they would be a viable more-native alternative to the American hatchery’s coastal Eel River origin stock. They were fine sport, susceptible to dry flies.

The American River hatchery program uses coastal origin stock that spawn in winter. Many spawners enter the river in late fall when fishing is closed to protect spawning salmon. Fishing is open in winter spawning season. This female caught in January was likely actively spawning. Native steelhead are spring spawners.