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.

Salmon Drought Plan – there is no plan

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A Salmon Drought Plan (with implementation) is badly needed. For the past two years, what we had instead was delayed reaction, an ad hoc hodge-podge of underfunded bandaid actions that didn’t come close to protecting salmon. The state and federal agencies called this “real-time” response. Huge injury to salmon resources occurred, and the triage center was a dysfunctional “Mash” unit.

Subtitle C of Section 421 of H.R. 2983, Congressman Huffman’s bill1 on drought assistance and improved water supply reliability, provides for preparation of a California Salmon Drought Plan and $3,000,000 for implementation. The measures in the bill would be a reasonable beginning:

(a) SALMON DROUGHT PLAN.—Not later than January 1, 2016, the United States Fish and Wildlife Service shall, in consultation with the National Marine Fisheries Service, the Bureau of Reclamation, the Army Corps of Engineers, and the California Department of Fish and Wildlife, prepare a California salmon drought plan. The plan shall investigate options to protect salmon populations originating in the State of California, contribute to the recovery of populations listed under the Endangered Species Act of 1973 (16 U.S.C. 1531 et seq.), and contribute to the goals of the Central Valley Project Improvement Act (Public Law 102–575). The plan shall focus on actions that can aid salmon populations during the driest years. Strategies investigated shall include—
(1) relocating the release location and timing of hatchery fish to avoid predation and temperature impacts;
(2) barging of hatchery release fish to improve survival and reduce straying;
(3) coordinating with water users, the Bureau of Reclamation, and the California Department of Water Resources regarding voluntary water transfers, to determine if water released upstream to meet the needs of downstream or South-of-Delta water users can be managed in a way that provides additional benefits for salmon;
(4) hatchery management modifications, such as expanding hatchery production of listed fish during the driest years, if appropriate;
(5) increasing rescue operations of upstream migrating fish; and
(6) improving temperature modeling and related forecasted information to predict water management impacts to salmon and salmon habitat with a higher degree of accuracy than current models.

However, Congressman Huffman’s bill, proposed as part of an alternative to still-pending legislation that would make conditions for fish worse, has not moved forward.

Why is it left to a California congressman to try to get a drought salmon program going? The state and federal resource agencies have huge staffs that are more than capable of taking action and immediately preparing a joint plan of action. Government grant programs have funded numerous NGO scientists who could participate. The state has a drought plan for cities and farms. Why isn’t there one that protects the state’s salmon resources? CDFW’s drought planning effort is outdated.2 There is no federal plan. For the past two years, the fisheries agencies have simply concurred with every Temporary Urgency Change Petition to weaken fish protections coming from the California Department of Water Resources and the Bureau of Reclamation, leaving protection of resources to the State Water Board (which also failed to step up).

California needs a salmon drought plan now.

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 .

A Foolish Proposal to End the Restoration of San Joaquin River Spring Run Salmon

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In a recent editorial,  the Fresno Bee editorial board1 stated that restoring salmon near Fresno in the San Joaquin River below Friant Dam is a “fool’s errand.”  The editorial referred to recent events near Shasta Dam on the Sacramento River:  “This decimation (of Sacramento Winter Run salmon) has occurred despite the best efforts of federal officials to save salmon – and at the expense of irrigation water for farmers. Officials, in fact, sharply curtailed water flows out of Lake Shasta last spring in an attempt to keep sufficient cold water in the system to support the fish.”  The editorial further stated: “If the Sacramento can’t sustain healthy salmon runs without crippling farmers, what are the prospects that the San Joaquin River – with less water and higher temperatures – can flow with spring-run salmon again?  The editorial implies that it is a waste of time trying to save salmon, especially San Joaquin salmon, “at the expense of irrigation water for farmers”.

Well, the Fresno Bee’s editors are wrong.  Both salmon populations can be restored.  The feds’ efforts at Shasta were in fact not their best.  Yes, most of the Winter Run Salmon died in 2015 as in 2014, but the salmon could have been saved (see our recent post).2  Farmers weren’t “crippled” by salmon: there was simply too little water to supply farmers, especially south of the Delta based on water right allocation priorities.  No additional water could have been released from Trinity or Shasta without jeopardizing next year’s water supplies (or salmon).  In both 2014 and 2015, the Sacramento River Settlement Contractors got most of their allocation (75% – over 1 MAF including water from Trinity Reservoir); at the end of 2015 in particular, many transferred water south of Delta.  Again, this was hardly crippling.  The Settlement Contractors could have and should have been allocated less.  They would have survived.  The salmon did not.  The salmon died from mismanagement of the water supplies and hydropower system, and because the managing agencies deliberately allowed water temperatures to stay for months above the safe level for incubating eggs.

There is no reason healthy salmon runs cannot be sustained in both rivers.  Most of the water released for salmon will still go to farmers.

Here is the best strategy for San Joaquin River salmon.

  1. Spring Run Salmon Only – There is a unique opportunity in this program to keep Fall Run and Spring Run apart to allow the native Spring Run to recover. Do not haul Fall Run salmon to the upper river or include Fall Run in the conservation hatchery.
  2. Conservation Hatchery – The San Joaquin needs a conservation hatchery to raise Spring Run salmon of an appropriate genetic stock for the San Joaquin. Such a facility is planned but so far it is only an “interim facility.”3   It is called the Salmon Conservation and Research Facility (SCARF).4  Its plan calls for using Feather hatchery spring run eggs.  That is a problem – the hatchery must start with eggs from native Central Valley stocks (Deer, Mill and Butte creeks), not “summer run” hybrids from the Feather River.  Yes, the San Joaquin is warmer, which is why having Feather “spring run” that migrate in May and June is not a wise choice.  March-April is a better time for adult upstream migrations in the San Joaquin, which is the timing the Deer, Mill and Butte creek stocks can provide.  The program review team recognizes this:  “Moving forward, there is a program goal of reintroducing multiple stocks from more than one spring-running population available, but there are a lot of questions that need to be answered from a genetics standpoint, in order to make sure reproductive success and survivability of progeny is maximized using pedigree-based genetic marking techniques.”5  The draft EIR (p. 6-57) for the new hatchery argues against using eggs from Deer,Mill or Butte creeks as it poses a threat to the  Deer, Mill and Butte creek populations:  “Propagation of fish at the SCARF has the potential to unintentionally change the genetic composition of wild populations and subsequently contribute to reduced survival in natural environments if conservation stock stray into the Sacramento River basin and spawn with wild spring-run stocks. Additionally, conservation stock may stray into other tributaries of the San Joaquin River basin and interbreed with fall-run Chinook, which may interfere with existing wild and hatchery management actions and reduce genetic fitness of these fall-run populations.”6  I contend that using Feather “spring run” that are already “compromised” genetically would pose a greater threat to other Central Valley stocks.  The technical review team seems to recognize this.  The federal Salmon Recovery Plan has a goal of adding more stock diversity to the Central Valley salmon populations to reduce the threat of extinctions.
  3. Trap-and-Haul – The young salmon produced by the conservation hatchery or produced by wild spawning salmon near Fresno should be trapped and hauled to the Bay except in wet years when river flows are high and the lower river is connected. The present plan is to trap the young and transport them for release near the mouth of the Merced River.  Most of these fish would not survive downstream passage through the lower San Joaquin and the Delta except in high flow wet years.  The young fish should be “barged” in boats with live wells and recirculating river water to ensure they continue imprinting on the San Joaquin.  This avoids many problems discussed in the Issue Paper on Delta effects.7
  4. Winter-Spring Pulse Flows in Wet Years – Young Spring Run would migrate downstream to the Bay and Delta from December to February as fry and fingerlings, and March and April as pre-smolts. Adults would migrate upstream in March and April.  In wet years with substantial natural connection, river flows and water supply, supplemental reservoir releases could be made to improve migration survival.  Such conditions may occur after or between storms, or simply to enhance storm flow peaks of less than adequate magnitude.  Such added flows could be coordinated with Sacramento flows and Delta conditions.  Delta conditions (Delta exports, Head of Old River Barrier, and Delta Cross Channel operations) could also be modified to help young San Joaquin salmon in wetter years when they would be passing through the Delta, and in all years when adults pass through the Delta.

As well as being a legal requirement and the correction of a grievous moral injustice, restoration of Spring Run salmon remains a viable goal for the San Joaquin River.

Scott River Chinook Crisis

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Klamblog1 recently reported that the Scott River Chinook salmon are again delayed from ascending the lower Scott from the Klamath River because of low water flow. This major Klamath tributary to the west of Mt. Shasta and Weed, CA that flows most winters with thousands of cubic feet per second (cfs) from rain and snow from the Trinity and Marble mountains has been flowing at less than 10 cfs this summer and fall. The salmon simply cannot migrate up this large, steep river with such low flow, especially in dry years when there is no snowmelt after June. The salmon simply wait for rain at the mouth of the Scott. Rains often come by December, just in time for California’s last viable run of Coho salmon, but too late for the Chinook.

As usual the blame is on irrigators in Scott Valley who draw down the water table with heavy groundwater pumping and surface water diversions in the summer for hay and pastures. The State Board did restrict most surface diversions this summer, but with little snowpack there was little streamflow to restrict. Scott Valley often has high groundwater, but with little snowpack recharge, less flood irrigation, and heavy pumping, groundwater seepage and ag returns to the river have virtually ceased, leading to the low flows.

Surprisingly, there is a solution that ranchers are willing to do – pump groundwater into the river in the fall after the summer irrigation season. There is more than enough pumping capacity and groundwater available. Ranchers only want payment for the electricity – a reasonably modest cost. In years like this we are talking about 8 to 10 weeks of a nominal amount of pumping and groundwater storage with a high likelihood that the groundwater used would be replaced/recharged this coming winter and spring.

The concept and proposal have fallen on deaf ears, and the ranchers have circled their wagons much like the salmon in the video link below. As the political fight over water goes on, we should take every opportunity like this one to save the salmon from extinction.

 

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.