Category Archives: Steelhead

Yuba River Fisheries Enhancement

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Improving Yuba River Fisheries

The Yuba River (Figure 1), including the lower river below Englebright Dam and its three upper forks and two reservoirs, provides a substantial fisheries resource. But it could provide much more.

Overall, the Yuba has a long complicated story with a colorful history that goes back to the gold rush and hydraulic mining in the last two centuries. Nearly two decades ago the CALFED program took on the Yuba fisheries as a special case.1 Options in these management planning efforts have included building a hatchery, trucking salmon and steelhead above the dams, removing dams, providing better upstream passage at dams, raising young salmon in rice fields, and enhancing spawning and rearing habitat in the lower river below Englebright Dam. Last year the National Marine Fisheries Service published its Central Valley Recovery Plan for threatened and endangered salmon and steelhead that included actions for the Yuba River.2 As prescribed in the Recovery Plan, The Yuba Salmon Partnership Initiative recently came to an agreement to trap and haul salmon above New Bullards Bar Reservoir to the North Yuba.3 The US Army Corps of Engineers and Yuba County Water Agency have also teamed up to enhance fish habitat and passage, and recently asked for public input.4 Their responsibility stems from the dams, flood control, water supply, and hydroelectric production on the Yuba River.

Yuba River Map

Figure 1. Yuba River is a tributary of the Feather River in the Sacramento Valley north of Sacramento, California. The lower river flows about 25 miles from Englebright Dam to to its mouth on the Feather River. New Bullards Bar reservoir on the North Yuba completed in 1970 is one of the largest in California, with storage of 966,000 acre-feet.

Status of Fisheries

Lower Yuba Trout Fishery

The gem of the Yuba is its lower river “blue-ribbon” wild trout fishery that extends from Englebright Dam downstream to Daguerre Dam and below, a total of about 20 river miles. The trout here are predominantly wild, except for some stray Feather hatchery steelhead smolts that migrate up from the Feather River, and for wild and hatchery trout from upriver that pass downstream from the dams. The wild trout of the lower Yuba have their own distinct character, likely derived from mixed genetics including steelhead. They grow quickly due to year-round near-optimal water temperature and to abundant tailwater insects supplemented with salmon eggs and fry. Trout survive well in the reach between Englebright Dam and Daguerre Dam in part because striped bass and other predatory fish cannot ascend Daguerre’s ladders. They are also protected by strict sport fishing regulations that limit gear, harvest, and season.

Lower Yuba Steelhead Fishery

The lower Yuba steelhead fishery is very limited, made up of small numbers of Feather hatchery strays and a very few wild steelhead. It is much the same case as in the lower Sacramento River near Redding, where wild resident trout dominate the fishery. There is no steelhead stocking on the lower Yuba, although many Feather hatchery steelhead smolts migrate into the lower Yuba and take up residence.

Spring Run Chinook Salmon

The number of spring run Chinook is also small, and is made up mostly of stray Feather River hatchery fish. Small numbers of adult spring run spend the summer milling below Englebright dam waiting to spawn in early fall. The population suffers from the flawed “summer run” genetics of the Feather River hatchery program, lack of spawning habitat below Englebright, and competition and interbreeding with fall run in the lower Yuba.

Fall Run Chinook Salmon

Abundant some years and not in others, the fall run salmon follow the trends of the Feather hatchery fall run, mainly because they are mostly Feather hatchery strays or their offspring. Like other Central Valley fall run, production suffers severely in drier years when winter flows are low and unable to carry newly emerged fry to their nursery areas in the Delta and Bay. Habitat and survival is poor for fry that remain in the rivers because of a lack of backwater and floodplain habitat and woody in-stream cover. The Yuba, like the Sacramento and its other tributaries the Feather and American, and like the San Joaquin and its tributaries, suffers from winter-spring reservoir storage of most of the dry year runoff, leaving little flow to help young salmon emigrate or to provide floodplain rearing habitat.

Recommended Actions

I recommend the following actions to help improve the populations of the target fish species to protect them from extinction, but also to improve the dependent sport and commercial fisheries.

  1. Adult Spring Chinook should be captured at Daguerre Dam and trucked above the dams to spawn. Young thus produced should be captured and transported below Daguerre Dam in wetter years or trucked to Verona (mouth of Feather River) and barged to the Bay in drier years. Spring run should not be allowed to spawn in lower Yuba where they interbreed with fall run or have their redds destroyed by fall run spawners.
  2. Spawning and rearing habitats in the lower Yuba should be enhanced as proposed in the above-described programs. Of greatest need are woody cover in low flow channels and low flow spawning and rearing habitats such as alcoves, side channels, and connected oxbows.
  3. Winter-spring flows in the lower river should be enhanced when necessary to improve emigration of young salmon and steelhead in wet, normal, and below normal water years given sufficient reservoir inflows and storage supplies.
  4. In dry years, wild fall run salmon and steelhead young should be captured in winter and spring at Daguerre Dam and trucked to Verona and then barged to the Bay.
  5. A conservation hatchery should be considered for the lower Yuba to enhance the spring run salmon and steelhead populations. Alternatively, repurposing of a portion of the Feather River Fish Hatchery to achieve this enhancement should be considered The first order of business would be to develop appropriate genetic stocks; the second would be to increase production and contribute to sustainable fisheries.

These and other suggestions are also generally prescribed in the following blog post by Dr. Peter Moyle (UC Davis): http://www.ppic.org/main/blog_detail.asp?i=1890 .

Trap and Haul –a better Central Valley option

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Last month, CalTrout’s blog had a post on a federal government program to trap-and-haul salmon and move them upstream of Shasta Reservoir.1 Earlier we also commented on trap-and-haul (http://calsport.org/fisheriesblog/?p=334). The National Marine Fisheries Service’s (NMFS) Recovery Plan for Central Valley Salmon and Steelhead prescribes trap-and-haul, as does their biological opinion for operation of state and federal Central Valley water projects.

Transporting adult salmon above dams and the offspring back below the dams is an expensive and difficult task. No one loves trap-and-haul, but NMFS considers it necessary to ensure that endangered salmon and steelhead do not go extinct. The prescription comes out of frustration that the populations are declining below the dams. Given the choice of extinction or doing something that no one is thrilled with, NMFS has chosen a set of actions in the latter category. The feds have again begun raising Winter Run Chinook in the fish zoo at Livingston Stone Hatchery to ensure there is some genetically pure stock available in the future. Having a wild stock above Shasta in the McCloud River seems a wiser option, given that those fish would be wild even if they spend some time in a truck. It is a further hedge against conditions like the past two years when the Bureau of Reclamation failed to keep their promise to protect the Winter Run downstream of Shasta.

NMFS has also prescribed trap-and-haul to pass Spring Run Chinook and Steelhead around Shasta Reservoir and other Central Valley dams. Stakeholders on the Yuba are developing a plan to carry out the prescription.

In a second blog post, CalTrout recently asked: “Will winter run go the way of the bull trout?”2 Most assuredly, trap-and-haul can help maintain populations while we get our act together below the dams. It’s a better option than a zoo.

Knights Landing Outfall Gates New Screens – Only a Start

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A SacBee article on October 22, 20151 describes the nearly completed Knights Landing Outfall Gates (KLOG or Outfall Gates) screening project on the Sacramento River: “local, state and federal officials are close to completing a $2.5 million project that will block an entrance wayward salmon use to get into the Colusa Basin Drain”. The operative word here is “an”, because the other entrance, and by far the more important, is the Knights Landing Ridge Cut (KLRC or Ridge Cut) outlet into the upper Yolo Bypass (Map 1).

Upstream-migrating Winter Run Chinook Salmon bound for spawning grounds below Shasta Dam near Redding in the Sacramento River can be attracted into irrigation and stormwater drainage system outfalls and eventually lost. The two largest outfalls are the Yolo and Sutter bypasses (see my previous blog on the bypass attraction – http://calsport.org/fisheriesblog/?p=421 ). Of lesser importance are a series of agricultural outfalls from low-lying basins adjacent to the Sacramento River. Chief among these are the Knights Landing Outfall Gates, which drain the Colusa Basin on the west side of the Sacramento River Valley.

The new screens on Outfall Gates will ensure that no salmon leave the river for the basin through the gates. But that is not the big problem. The Colusa Basin Drain (CBD or Drain) is also a stormwater drain that can flow mightily in winter storms even in drought years such as 2013-2015 (Charts 1 and 2). When stormwater-driven high flows in the Drain occur, the Outfall Gates’ outlet is usually closed because the river is higher than the gates during storm runoff. Under these high flows, water in the Drain is forced down the Knights Landing Ridge Cut into the upper Yolo Bypass (see Map 1).

Storm runoff that passes through the Ridge Cut into the Yolo Bypass attracts many salmon, steelhead, and sturgeon into the Drain and to their eventual demise in the dead-end Colusa Basin. Storm flow to the Yolo Bypass reaches 4000-6000 cfs in drought years, while non-storm flows through the Outfall Gates are usually only several hundred cfs (Charts 1 and 2). Flows leaving the Yolo Bypass and entering the Delta at Cache Slough (Map 2) attract many salmon, steelhead, and sturgeon moving through the Delta. During floods, the Sacramento River spills into the Yolo Bypass, adding even more attraction flows through Cache Slough. With limited passage options past the Fremont Weir at the upper end of the Yolo Bypass (Map 1 or 2), many of fish moving up the Yolo Bypass are attracted to and migrate up the Ridge Cut.

In short, the Knights Landing Ridge Cut outlet also needs to be blocked to keep fish from migrating into the Colusa Basin and being lost. The threat is serious not only to Winter Run Chinook, but also to Fall Run, Late Fall Run and Spring Run Chinook, as well as Steelhead, Green Sturgeon and White Sturgeon. Fish passage facilities at Fremont Weir are also needed so that adult fish that migrate up the Yolo Bypass are not stranded in the Bypass.

Map 1

Map 1. Location of Knights Landing Outfall Gates (KLOG) on Sacramento River and Knights Landing Ridge Cut (KLRC) outlet in the Yolo Bypass near Knights Landing, CA. Red arrows point out routes taken by salmon into the Colusa Basin.

Chart 1

Chart 1. Flow in the Colusa Basin Drain Nov 2013 through May 2014. Red line depicts flow when KLOG were closed due to high Sacramento River stage. (At flows above about 900 cfs in the CBD the KLOG were closed and flow diverted to Yolo Bypass via KLRC.)

Chart 2

Chart 2. Flow in the Colusa Basin Drain Nov 2014 through May 2015. Red line depicts flow when KLOG were closed due to high Sacramento River stage.

Map 2

Map 2. Route salmon take from the Delta via Cache Slough up the Yolo Bypass when attraction flows are input from either the Knights Landing Ridge Cut or the Fremont Weir.

Loss of Salmon in the Sacramento River Floodplain

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The loss of juvenile and adult salmon in the Sacramento River floodplain has been a problem for many decades. The problem is largely the result of the construction of dams, agricultural drains, and flood control systems. The problem is acute, and although well documented and quite obvious, little has been done to resolve it. The fixes are not cheap and no one wants to get stuck paying for them. In addition, potential fixes have been hoarded as potential mitigations for large public works projects like the Bay Delta Conservation Plan and its associated Delta Tunnels.

The Problem

Figure 1 is a map of the Sacramento Valley with arrows showing some of the major locations of the problem. Much of the problem is the result of limitation or blockage of fish passage; another major factor is stranding. Adult salmon, sturgeon, and steelhead migrating up the Sacramento River become attracted to the high volumes of Sacramento water exiting the Sutter and Yolo Bypasses (adult fish movement is shown by red arrows in Figure 1), only to be blocked at the high weirs at the upstream end of the bypasses (Figures 2 and 3). Even modest bypass flows in drought years can cause attraction and subsequent mortality (Figure 4).

Young salmon emigrating downstream from upriver spawning grounds pass into the bypasses (green arrows in Figure 1) and adjacent basins in huge numbers. Many become stranded and lost when flows and water levels decline when weirs quit spilling (the river can drop ten feet overnight and quickly cease spilling into bypasses).

Landowners Seek Solution

In one of the areas, the Yolo Bypass, local landowners and stakeholders are seeking a solution. They are addressing three critical issues:

  1. Blockage of upstream migrating fish behind the Fremont Weir at the head of the Bypass.
  2. Blocked fish migrating to their deaths into the Colusa Basin from the Bypass via the Knights Landing Ridge Cut1. Adult migrants are also attracted directly to Colusa Basin Drain outlet even when Fremont Weir does not spill.
  3. Increasing survival of young salmon spilled into the Yolo Bypass by augmenting flows and improving habitats and habitat connectivity.

The first issue often occurs each time the weir spills at flood stage (generally one in three years, although it has not spilled significantly since 2006 because of drought). The bandaid treatment is shown in Figure 2. Stakeholders have advocated a short-term solution for passing fish via a “small notch” in the Fremont Weir to pass fish over the weir into the river; however, long-term agency plans call for a more contentious “large notch” in the weir.

The second issue requires the opposite solution, placing a fish-blocking weir at the outlet of the Knights Landing Ridge Cut to stop adult salmon, sturgeon, and steelhead from migrating upstream into the Colusa Basin. Landowners are working with the California Department of Water Resources and Reclamation toward building such a weir. For now the bandaid is a fish trap and fish rescues such as that shown in Figure 2.

The third issue can be resolved by engineering the bypass floodplain to provide better habitat and connectivity for the salmon including high and longer-sustained flows from the Fremont Weir (via a “notch”). Local landowners have developed an array of actions to provide habitat and connectivity.

In my experience, placing leadership and responsibility for developing and implementing actions in the hands of local stakeholders has worked best to help save fish. “Locals” can be surprisingly adept at coming up with viable solutions to fisheries problems.

Map of Sacramento Valley showing levees and flood control system weirs and bypasses

Figure 1. Map of Sacramento Valley showing levees and flood control system weirs and bypasses. Gray area agricultural basins are generally below the elevation of the river and bypasses. The flood control system was initially designed to convey flood water and historic foothill mining debris through the Valley. Adult salmon (as well as sturgeon and steelhead) are attracted to the high flows entering, passing through, and exiting the Sutter and Yolo Bypasses (such adult migration is shown with red arrows). Many cannot successfully complete their passage either becoming lost or blocked at the upstream end by weirs (located at the blunt end of the green arrows). Many young salmon become stranded in the basins and bypasses after entering in spill over weirs during floods. (Map source: http://baydeltaconservationplan.com/Libraries/Dynamic_Document_Library/Fact_Sheet_-_Sac_River_System_Weirs_and_Relief_Structures.sflb.ashx )

Figure 2. Sturgeon being rescued below a Sacramento River bypass weir

Figure 2. Sturgeon being rescued below a Sacramento River bypass weir

Moulton Weir 1997

High storm flows in late December 2014 into the Yolo Bypass from the Knights Landing Ridge Cut attracted many salmon to the northern end of the Bypass

Figure 4. High storm flows in late December 2014 into the Yolo Bypass from the Knights Landing Ridge Cut attracted many salmon to the northern end of the Bypass. When storm flows receded after several days, hundreds of adult salmon became stranded in winter-fallow fields that had been flooded. Many more salmon likely passed successfully into the Colusa Basin drain system only to find no route to spawning grounds in the upper Valley.

Trap-and-Haul of Salmon/Steelhead Around Instream Barriers

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By Don Beyer
Dams, impassable falls, and other instream barriers such as reduced flow, high temperature, poor water quality block or impede the migration of salmonids. The following are brief summaries of several case studies in Washington State where trapping and transport around these barriers has had encouraging results.

Recovery of Baker River Sockeye Salmon

Baker River is a tributary to the Skagit River in northern Washington State. Sockeye salmon have a very challenging life history in that they need a lake for young rearing prior to smolt outmigration to the ocean. Before the development of two hydroelectric dams, the native Baker Sockeye salmon used natural Baker Lake for spawning and rearing. After the two dams were constructed (the first dam, Lower Baker, was completed in 1925 below the lake, the upstream dam was completed at Baker Lake outlet in 1959) the sockeye salmon migrations were nearly completely blocked. Natural spawning habitat was destroyed upstream of the upper dam. The adult returns of sockeye salmon prior to the dams were estimated by the Washington Department of Fish and Wildlife1 to be about 20,000 fish but the returns fell to a low of about 99 fish in 1985.

Considerable efforts have gone into research and development of ways to facilitate both upstream and downstream passage around the two dams. The current efforts include improved trap-and-haul operation facilities below the lowermost dam, trucking to artificial spawning beaches (also newly improved) located on Baker Lake, and a new conservation hatchery next to the spawning beaches. Some adults are also released into Baker Lake to spawn naturally in Baker River and its tributaries upstream of the lake. Downstream smolt migration has been improved by trapping outmigrating smolts at both dams and transporting by truck for release below the lowermost dam. The outmigrant collection facilities have been upgraded with nets behind each dam that guide the outmigrants to the traps where they are collected and transported below the lowermost dam.

These improvements have resulted in a record run of 22,500 adult sockeye in 2010. The Washington Department of Fish and Wildlife2 forecast for returns in 2015 is 46,268 adults. The improved runs have resulted in removal of the Baker River sockeye from the Endangered Species Act candidate list. In addition, the current runs support both a tribal fishery (in downstream areas) and sport fishery (in downstream areas and in Baker Lake).

Adult Salmon/Steelhead Trap and Haul – South Fork Skykomish River at Sunset Falls

The South Fork Skykomish River joins the North Fork near Index, Washington. Combined, the two forks form the Skykomish River, which eventually flows into Puget Sound (as the Snohomish River) at Everett, Washington. This Snohomish River basin supports significant runs of coho salmon, Chinook salmon, chum salmon, pink salmon, steelhead, and cutthroat trout. Sunset Falls (near Index) is the first of three steep gradients that historically formed a totally impassable barrier to upstream migration of adult salmonids. The drainage area upstream of these barriers is about 350 square miles which has many mainstem and tributary areas that are favorable for spawning and rearing of anadromous fish.

The Washington Department of Fish and Wildlife (at the time they were the Washington Department of Fisheries) built a trap and haul facility below Sunset Falls in 1958. Trapped adult anadromous fish are captured and transported by truck to an area above the uppermost falls. These fish then migrate further upstream to spawn naturally.

The trap and haul approach has been in operation since 1958 and has passed an average of 25,000 total fish (all species) per year. This average has increased in recent years (to 46,000) due to large increases in pink salmon returns3.

Cowlitz River Fish Transport

The Cowlitz River is a major tributary to the Lower Columbia River that supports major runs of salmon and steelhead. Upstream passage of adult fish was blocked by construction of Mayfield Dam which began operation in 1963. Initial attempts to pass adults upstream were made by capturing adult fish below the dam and transporting them upstream. Outmigrants were passed around the dam through a bypass system. The situation became more complex when Mossyrock Dam (upstream of Mayfield Dam) began operation in 1968. At the same time, a barrier dam was constructed downstream of Mayfield Dam to channel fish into a newly constructed hatchery. This hatchery, one of the largest in the world, was mainly composed of concrete raceways for holding of adults and rearing of juveniles. In addition, another hatchery, primarily dedicated to production of steelhead, was constructed downstream. This hatchery has large rearing ponds for the juvenile steelhead rather than concrete raceways.

The operation of the barrier dam provided the opportunity to utilize fish for production in the hatchery or to move adults to upstream areas to naturally spawn. The challenge then was to have the outmigrants successfully migrate downstream through the reservoirs and dams.

The success of the two hatcheries has been monitored and evaluated over the years since they began operation until the mid-1990s. During this period, the mainstem below the barrier dam supported an intense sport fishery which in some years had been very good and other years not so good (mixed results that have been attributed to a number of factors including the fish handling/hatchery conditions, ocean survival, commercial/sport fisheries downstream, volcanic eruptions (i.e., Mt. St. Helens in 1980), and others). This fishery continues to the present day.

Although the fish management approach to the Cowlitz River evolved over a number of years, the situation changed when another dam (Cowlitz Falls Dam) was completed 1994. This dam is located upstream of the Mossyrock reservoir. With the current operation of the three dams, a new emphasis was placed on natural production of fish in upstream areas. Adults are transported from the downstream barrier dam to areas upstream of the Cowlitz Falls Dam where they can naturally spawn. They are also transported to the Tilton River, a tributary to the Mossyrock reservoir.

Outmigrating juveniles are funneled into bypass flumes at the Cowlitz Falls Dam where they are passed downstream to a fish collection facility. At the facility, fish are marked with various methods including coded wire tags implanted in the snout of the fish that allows for later identification. Some are radio tagged for research purposes.

Upstream migrating adults originating from above the dams captured at the barrier dam can then be transported above the Cowlitz Falls Dam with natural production (unmarked) fish. Fish marked originally at the hatchery can also be kept for production at that facility.

The Cowlitz River situation can best be described as an evolving process that is moving in a favorable direction. The fish management approach has maintained and, in some instances (such as increased limit sizes), improved the very active sport fishery in the downstream areas. Improvements in utilizing the areas upstream of the dams for natural production should assist in further expansion of the fisheries resources in the Cowlitz River basin while increasing natural production.