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.

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

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

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.

Hatchery Steelhead Smolts Released Just in time to Chow Down on Baby Salmon

The state and federal hatcheries in the Central Valley will be releasing 1.5 million yearling steelhead smolts this winter. The location and timing of these releases could not be worse for the survival of newly emerged wild fall-run and spring-run salmon.

The U.S. Fish and Wildlife Service released approximately 600,000 smolts from the Coleman Hatchery on Battle Creek into the Sacramento River near Redding in January. The California Department of Fish and Wildlife will release approximately 900,000 steelhead smolts from state hatcheries to the lower American, Feather, and Mokelumne Rivers in February. The peak of newly emerged salmon fry is January in the Sacramento River near Redding and February in the three tributary rivers (the difference is a result of managed fall water temperatures).

In prior posts,1 I warned of releasing yearling hatchery smolts on top of wild salmon fry (see photo below). The solution is to simply stop doing this. The fish agencies should release the mitigation hatchery smolts earlier or later in the year, or truck them to the Delta or Bay as they did in the past. In general, the agencies should also release steelhead smolts during high flows, when juvenile salmon have a greater chance to evade the steelhead, and when both steelhead and salmon are likely to move more quickly downstream.

In the longer term, the California Department of Fish and Wildlife and the U.S. Fish and Wildlife Service should redirect their steelhead hatchery programs toward recovery of the native steelhead stocks by converting their efforts to conservation hatchery programs. Many of the native steelhead traits are less intrusive on the salmon (e. g., fall and spring migrations, spring spawning). The fish agencies should also stop using stocks whose origin is out-of-basin (American River).

Photo: yearling hatchery steelhead smolt fed on wild salmon fry in American River in February. (Photo by author)

 

 

 

Sustaining wild Salmon and Steelhead above Central Valley dams

The Case for Two-Way Trap and Haul

Why should we expand spawning populations of listed salmon and steelhead to areas above dams and impassible falls in the Central Valley? The answer is: because the genetic makeup and wild traits of populations upstream of existing barriers can be controlled, restored, and preserved.

At present, the genetic makeup of salmon and steelhead populations below dams is continually being compromised by hatchery fish and strays to and from other watersheds. The one population of winter-run Chinook is confined to the spawning reach immediately below Keswick Dam and thus is subject to the potentially drastic whims of nature and man. That population is further being compromised by the increasing threat of hatchery degradation of the gene pool as winter-run hatchery fish further dominate the adult spawning population. Small, self-sustaining populations of spring-run Chinook and steelhead remain in only a few watersheds. They too are continually being threatened by strays and hatchery fish.1

One solution to maintaining genetic integrity by limiting genetic influence from hatchery-produced fish and interbreeding of genetically or behaviorally distinct runs is to implement trap-and-haul programs in isolated reaches above dams.

The National Marine Fisheries Service included requirements to establish winter-run Chinook trap-and-haul populations above Shasta Reservoir in 2009, 2010, and 2014 biological opinions on Central Valley Project (CVP) and State Water Project (SWP) operations. CALFED proposed introducing spring-run Chinook above Yuba River dams. Extensive studies have been conducted on reintroducing salmon in these areas. The requirement to establish populations upstream of Shasta has been dropped in the Trump administration’s October 2019 biological opinion for the CVP and SWP. For the moment at least, the requirement remains in state of California plans.2

The California Department of Fish and Wildlife’s California Endangered Species Act Take Permits for CVP and SWP operations should require reintroduction of salmon and steelhead upstream of an array of dams in the Sacramento River watershed. All of the sites I recommend are affected by the CVP and SWP. The state should also consider locations in the San Joaquin and Klamath River watersheds. The Klamath watershed is also affected by Reclamation’s Klamath Project, and is the present subject of the country’s largest dam removal project.

In considering potential sites I focused on the ability to maintain experimental controlled conditions as well as optimum habitat quality sites. In most cases, that meant minimal flow variation and high quality, cold reaches dominated by spring water. The sites need not be in the historical range, but should be in historically occupied watersheds (e.g., they could be upstream of impassible falls in watersheds that historically held salmon and steelhead.).

I suggest five sites in the Sacramento River watershed (Figure 1).

  1. Upper Sacramento River (above Lake Shasta) – below Lake Siskiyou dam upstream of Dunsmuir in the Box Canyon/Shasta Springs reach.
  2. Upper McCloud River (above Upper McCloud Falls) – spring-fed reach above Larkin Dam on south flank of Mt Shasta.
  3. Upper Battle Creek – Ripley Creek, tributary of South Fork, spring-fed, although presently its flow is diverted by PG&E to South Fork Powerhouse.
  4. Upper North Fork of Feather River – above or below Lake Almanor.
  5. Upper North Yuba River – above Bullards Bar Reservoir.

I have studied all of these sites and consider them feasible for reintroduction. Most have been considered for reintroduction by state and federal resource agencies. Reintroduction strategies may include releases of native-strain adult spawners, planting of eyed eggs, fry, or fingerlings, then capture and trucking to locations downstream of dams.

For more on reintroducing salmon above dams see:
https://podcast.barbless.co/reintroduction-of-winter-run-chinook-into-the-mccloud-river-jon-ambrose-noaa-nmfs/

https://www.webpages.uidaho.edu/UIFERL/pdf%20reports/Keefer%20et%20al.%20%202010%20WIL%20Chinook%20prespawn%20mortality%201.pdf

https://fishwithjd.com/2015/05/07/new-plan-developing-to-get-spring-chinook-into-north-yuba-upstream-of-bullards-bar-reservoir/

Figure 1. Historical range and present range of salmon in Sacramento-San Joaquin watershed, with suggested five locations for reintroduction via two-way-trap-and-haul shown as red dots.