Welcome to the California Fisheries Blog

The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.

Feather River Salmon Recovery Responsibilities, Commitments, and Recommendations

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  The Feather River’s once-prolific populations of wild spring-run and fall-run salmon have been replaced by smaller numbers of hatchery fish of inferior genetic composition.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.

Reclamation Has Done Everything it Could to Kill off Salmon this Summer. Now it Plans to Finish the Job.

The Bureau of Reclamation’s plan for Shasta-Trinity operations in summer of drought year 2021 was founded on killing off the salmon in the upper Sacramento River to sustain hydropower and water deliveries. So far, it has been wildly successful. Now Reclamation plans to finish the job on winter-run, spring-run, and fall-run salmon.

First, in late April and early May, Reclamation released an extraordinary amount of warm water from Shasta Reservoir for contractor water deliveries. These early releases compromised and delayed early winter-run spawning and late season smolt migration to the ocean (#1 in Figure 1). The early releases also unnecessarily reduced already critically-low Shasta storage, compromising the summer storage and cold-water-pool supply.

Second, Reclamation’s late May and early June releases of colder water (it ceased warm surface releases) encouraged spawning under falling flows, dropping river stage, and marginal spawning temperatures (Figures 1 and 2).

Third, increasing cold-water releases in late June and July (Figure 1) encouraged further spawning under rising and higher water levels (Figure 2).

Now, Reclamation plans to reduce releases of water in August and September (Figure 1). The water will get steadily warmer, because most of the cold water is gone. The combination of warm water and sharply dropping river stage (Figure 2) will complete the demise of this summer’s delayed winter-run spawn. The warmer water temperature will kill the late spawned eggs/embryo. A 4-foot drop in water level will strand and dewater many of the redds. The loss of Shasta’s cold-water-pool will also compromise the spring-run and fall-run spawning runs.

And finally, Reclamation will draw Shasta Reservoir down to historically low levels this fall. This will place Reclamation in a great position to kill all the salmon next year, too.

Figure 1. Flow and water temperature below Keswick Dam in the upper Sacramento River near Redding through late July 2021, along with Reclamation’s projections for August-September.

Figure 2. River stage below Keswick Dam in the upper Sacramento River near Redding through late July 2021, along with Reclamation’s projections for August-September.

 

Shasta Dam Update – July 18, 2021

There is still time to take action needed to save some of this year’s salmon production in the Sacramento River.1 Reclamation must immediately stop its irresponsible operation and revert to a maximum 5000 cfs Shasta Dam release, with no release from the middle gates and with minimal peaking power releases or input from Whiskeytown Reservoir.2

Here is the situation right now:

  • The last two weeks of July in the spawning reach near Redding will have daily average air temperatures over 85ºF, with highs of 100-107ºF.
  • Shasta Reservoir is losing 10,000 acre-feet and ½ foot of water-surface elevation per day, due to excessive storage releases (Figure 1).
  • Lower elevation dam release gates are about to go above the top of the cold water pool (Figure 2). This will reduce Reclamation’s ability to sustain cold-water releases through the summer for downstream salmon.
  • Peak power releases draw warmer water from surface layers (Figure 3).
  • Release of warmer 56-57ºF water from Whiskeytown Reservoir via Spring Creek Powerhouse into Keswick Reservoir further compromises Shasta’s cold-water pool3 (Figure 4)
  • As Reclamation had predicted in its Temperature Management Plan, the bottom side gates will have to be opened to sustain cold water releases by mid-August, which will accelerate the loss of the cold-water pool and compromise cold-water dam releases.
  • Diversions from the Trinity via Whiskeytown are getting warmer, requiring more of Shasta’s cold-water to overcome warming of Shasta/Keswick reservoir releases.
  • Shasta’s warmer peaking power water also requires more cold-water pool water to maintain the target <54ºF Keswick Dam release temperature.

It is essential to maintaining cold-water releases from Shasta Dam into early October to save winter-run salmon reproduction in this critical drought year. Cold water ran out in the summers of 2014 and 2015, and the winter-run salmon runs plummeted.4 Recovery of this critically endangered species5 requires an all-out-effort to protect the survival of eggs and embryos over the summer in the 10-mile spawning reach below Shasta and Keswick dams.

Conclusions and Recommendations

  1. Releases from Whiskeytown Reservoir (Trinity River water) should be minimized, because the 2000 cfs of 56-57ºF water must be neutralized with water from the Shasta cold-water pool. It is taking about 1000 cfs of 48ºF water from Shasta to keep Keswick releases less than 54ºF. Eliminating the import of Trinity River water would save 2000 acre-feet of Shasta storage and cold-water pool volume each day. That would save over 100,000 acre-feet of Shasta storage and over 200,000 acre-feet of Trinity storage by the end of September.
  2. In addition to the cutting the Shasta release by 1000 cfs by discontinuing the need to offset warm Whiskeytown water, Shasta releases should be cut a further 1000 cfs by shutting off warm water from the middle gates (see Figure 2). This would further preserve the volume of the cold-water pool and save an additional 100,000 acre-feet of Shasta storage.

These actions would allow a 5000 cfs releases of <54ºF water from Keswick Dam through September, which would save a significant proportion of the endangered Winter-Run Chinook salmon. It would also save nearly 400,000 acre-feet of reservoir storage for water year 2022.

Figure 1. Shasta Reservoir inflow, outflow, and storage, 1-16 July, 2021.

Figure 2. Shasta Dam operations scheme and reservoir conditions during the first week of July 2021. Note middle remain open to accommodate peaking power releases and high downstream irrigation deliveries.

Figure 3a

Figure 3b Figure 3a and 3b. Hourly water temperature (a) and flow (b) release pattern from Shasta Dam during first half of July 2021. Note most peaking-power releases are in afternoon and evening hours, with water temperatures several degrees higher during the daily peak generation. Daily average releases were 6500-7500 cfs, with peaks on the 6th and 9th.

Figure 4a

Figure 4b Figures 4a and 4b. Hourly water temperature (a) and flow (b) release pattern from Whiskeytown Dam during first half of July 2021. Note most peaking-power releases are in afternoon and evening hours, with water temperatures in the middle range of the daily pattern or about 1ºF below the daily maximum. Note the base flow of 250 cfs is to Clear Creek, with the remainder to Spring Creek powerhouse on Keswick Reservoir. Also, note peak releases to the Spring Creek powerhouse were about 3500 cfs for 12 hours from July 3-8. Daily average releases rose from about 1000 cfs on July 1 to 2000 cfs on July 4, then dropped to 1500 cfs on July 11, only to increase again through July 15.

 

 

  1. As much as 50% of spawning may yet occur. See https://escholarship.org/uc/item/00c1r2mz 
  2. This is an update from my late June report on Shasta Dam operations.
  3. It takes about 1000 cfs of Shasta’s cold-water pool to cool 2000 cfs of 56-57ºF Whiskeytown water.
  4. https://www.fisheries.noaa.gov/feature-story/endangered-winter-run-chinook-salmon-increase-millions-offspring-headed-sea
  5. https://www.fisheries.noaa.gov/video/species-spotlight-sacramento-winter-run-chinook-salmon

State Water Board to Decide Fate of Shasta and Scott River Salmon and Steelhead – Part 3, the Shasta River

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.  Part 2 provided specific comments on the Scott River.  This is Part 3 on the Shasta River.

The Shasta River Problem

The Shasta River, like the Scott River, has a chronic streamflow problem that occurs in summer and fall of most years.  Only in very wet years, do flows sustain the needs of ranchers and fish for water.  In most dry years, nearly all the water in the watershed goes to agriculture, while  the lower river and most major tributaries run virtually dry (Parks Creek, Little Shasta River, Yreka Creek).  Salmon and steelhead survive during dry years only in the middle reaches of the mainstem Shasta River and in adjoining large springs fed by Mt. Shasta’s snow fields or leakage from Lake Shastina reservoir.

At the locations in the watershed that are watered by springs, large portions of the spring-fed flow are diverted for agriculture or other human use (e.g., bottled water, domestic use, cities, etc.).  Pasture irrigation, hay production, and stock watering are the major uses.  Much of the upper mainstem’s  water supply (both spring-fed and snowmelt) is stored in Lake Shastina and metered out over the summer for downstream use through a large canal and ditch irrigation system.  Big Springs, the dominant source of spring water to the middle and lower river, is diverted or pumped to irrigation ditch systems from several small diversion dams and multiple small distribution systems.

Most salmon and steelhead spawning and rearing occurs in the middle reaches of the river below Lake Shastina and in the reach near Big Springs, where spring-fed cold-water provides high quality spawning and rearing habitat.  The inputs of spring water in summer of drier years like 2021 are virtually gone by the time river water reaches Yreka (Figure 2) from the above mentioned extraction systems.  The base flow of approximately 150 cfs before the April 1 start of the irrigation season falls to 10-20 cfs or lower by summer.  Flow recovers after the irrigation season ends on October 1.  Most of the irrigation diversions in the mainstem Shasta River are located in the 10-20 miles downstream of the inflow from Big Springs, as is evident by at the streamflow gage near Montague (Figure 3).

Lower flows lead to high water temperatures in the lower river (>65ºF, Figure 4) that limit fish habitat, survival, and smolt production. Unlike the Scott River, dewatering and stranding are not a primary factor in the middle river’s spring-fed refuge.  Rather, the problem is high water temperature between Grenada and the Shasta River’s mouth at the Klamath River.  Historical water temperature records at the Yreka gage (Figure 5) indicate that the lower river is virtually uninhabitable in summer with water temperatures 20-25ºC because of low streamflows.  Historical data from the Montague gage indicate tolerable water temperatures (<20ºC) when streamflows are >50 cfs (Figure 6).   Such flows and water temperatures would at least provide minimum requirements for migrating adult fall run Chinook salmon in late summer.

Solution Option for the Shasta River

CDFW’s recommended minimum instream flows of 50 cfs (about a third of the base flow) is a reasonable measure that would maintain a modicum of over-summer rearing habitat in the spring-fed middle reach of the Shasta River and provide the opportunity for the late-summer salmon migration.   The major objective is to protect the many spring inputs in middle reach of the river, where most over-summer rearing of salmon and steelhead occurs, through summer season.  This can be accomplished by cutting back diversions and groundwater pumping in the Big Springs area, and by minimizing warm, polluted irrigation return water.

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 2. Shasta River daily-average streamflows at Yreka gage 2018-2021 and historical average. Note very low flows in April 1 to October 1 irrigation season in 2020 and 2021. Base flow from large springs is approximately 150 cfs. Lower flows are from surface and groundwater extraction.

Figure 3. Streamflow in Shasta River at Montague gage 2019-2021. Note distinct reductions in April 1 to October 1 permitted irrigation season.

Figure 4. Water temperature of Shasta River at Grenada 2019-2021. Note water temperature increase at beginning of irrigation season on April 1 and decrease at end near October 1.

Figure 5. Streamflow and water temperature (min-max) of Shasta River near Yreka CA, March-October 2003.

Figure 6. Streamflow and water temperature (min-max) of Shasta River near Montague CA, May-July 2008.

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

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.