Category Archives: Water Quality

Spill and Salmon Survival

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In an earlier post, I suggested “spill” to help recover salmon in the Central Valley. Spill is nomenclature used for reservoir releases. In this case I refer to spill as reservoir releases to help juvenile salmon emigrate from spawning reaches below dams to the ocean. On the Columbia River, “spill” refers to reservoir releases around hydropower turbines usually through spillways. Such spills have been used successfully on the Columbia River to avoid turbine passage that may kill young salmon and to create flows through and below reservoirs to reduce young salmon mortality by shortening their emigration time. On the Sacramento and other Central Valley rivers, “spill” releases can go through hydropower turbines because young salmon start their emigration below the dams. Young salmon have been found to emigrate during flow pulses, with survival directly related to the amount of flow.

More “spill” below the rim dams is needed in the Central Valley to increase survival of naturally produced (wild) salmon and steelhead. Spills help young salmon emigrate from tailwater spawning and rearing reaches below dams to the Delta, Bay, and ocean. Both timing and magnitude are important. Timing relates to when the young salmon are ready to migrate and to natural flow pulses in the Valley. Magnitude is simply how much flow, which relates to precipitation and available reservoir storage supply.

Timing

Most of the Chinook salmon runs emigrate to the San Francisco Bay-Delta as fry soon after hatching. Some migrate as sub-yearling fingerlings and smolts1 while a few migrate as yearling smolts.

Winter Run Salmon

Winter Run hatch in late summer and early fall in the Sacramento River below Shasta and Keswick reservoirs. They usually emigrate as fingerlings and pre-smolts to the Delta when the river cools, especially during the first flow pulses in late fall and early winter. In drier years they may not emigrate until February or even March. Generally they move down to the Delta in the first flow pulse in December (Figure 1).

Late Fall Run Salmon

Late Fall Run also hatch in winter in the Sacramento River below Shasta and Keswick reservoirs. They usually emigrate as yearling smolts in late fall or early winter, at the same time as the Winter Run. Unlike Winter Run, they are often fully developed smolts and thus migrate quickly to the ocean.

Spring Run Salmon

Spawned in early fall, Spring Run hatch and migrate as fry and fingerlings with the first pulse of flow in late fall and early winter. Some migrate as presmolts and smolts in spring.

Fall Run Salmon

Spawned in fall, Fall Run hatch and emigrate as fry in winter during flow pulses. Some emigrate as fingerlings and pre-smolts in spring.

Catch index graph

Figure 1. Older Juvenile Catch Index for the Knights Landing rotary screw trap October through March 2000-2003. Older juveniles are generally Winter Run and Late Fall Run. (Source: http://www.science.calwater.ca.gov/pdf/ewa/support_docs_110804/ Salmon%20Criteria%20Figures%201_2_Chappell.pdf)

Steelhead

Steelhead spawn in winter and spring and emigrate as smolts after rearing in Valley rivers for one to three years. They migrate to the ocean during winter and spring flow pulses.

Spill Recommendations

To illustrate my recommendations, I focus on 2015 – a drought year with very limited reservoir supply and managed spill potential. Such years would be considered worst case scenarios for applying spill prescriptions. Yet despite limited potential in 2015, there were opportunities with the available supplies and precipitation to provide spill that would have substantially benefited salmon. Below are charts of flows for drought water year 2015 that depict the effects of two storm periods on Delta inflow and outflow. Delta inflow came primarily from runoff in un-dammed tributaries. Figure 2 depicts Delta inflow at Freeport with two distinct pulses of storm flow. These same flow pulses are apparent as Delta outflow to the Bay in Figure 3.

2015 Delta inflow graph

Figure 2. Delta inflow in water year 2015. (Source: CDEC)

2015 Delta outflow graph

Figure 3. Delta outflow in water year 2015. (Source: CDEC)

Below Shasta-Keswick in the lower Sacramento River, there was no winter storm flow (Figure 4). There were only two small managed flow increases of about 1000 cfs for three or four days each (a total of about 15,000 acre-ft), because Shasta held nearly all of its inflow from the two storm periods (Figure 5). Shasta inflow reached over 20,000 cfs for six days in each of the storms (Figure 6). Out of approximately 1,500,000 acre-ft of new storage inflow, Reclamation released only15,000 acre-ft (1%) of storm inflow for salmon.

A spill prescription of just 5% of inflow below Shasta-Keswick in the primary nursery for Winter Run salmon could have provided an increased 3000-4000 cfs of “spill” for seven days, instead of the 1000 cfs increases. Instead of going into the irrigation season at 2.72 million acre-ft, in storage, Shasta would have started at 2.67 million acre-ft. Given the potential benefit of the flow releases, this prescription even for a drought year is more than reasonable.

This example is for the fourth year of drought, when the reservoir began the winter at only 25% of capacity. In wetter years when storage is over 50% capacity, spills of 10% should be considered.

The same circumstances and potential benefits occur below other large Central Valley storage reservoirs, especially Oroville Reservoir on the Feather River and Folsom Reservoir on the American River. Spills of 5% in low storage years and 10% in higher storage years are reasonable prescriptions for their depressed salmon and steelhead populations.

Graph of Reservoir releases from Shasta-Keswick

Figure 4. Reservoir releases from Shasta-Keswick in water year 2015. Only two small releases were made in the storm periods.

Graph of Shasta Reservoir storage

Figure 5. Shasta Reservoir storage in water year 2015. The two storm periods added nearly 1.5 million acre-feet of water to the reservoir.

Graph of Shasta inflow

Figure 6. Shasta Reservoir inflow in water year 2015.

  1. Smolts are larger (3-6 inches in length) juveniles physiologically ready for entry to salt water. ↩

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 .

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.

 

Save the Winter Run Salmon

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By now most everyone has seen the newspaper articles on the catastrophic decline in Winter Run Chinook salmon production in the Sacramento River below Shasta Reservoir in 2015. The number of Winter Run juveniles passing downstream past Red Bluff is down substantially from last year, when the estimated survival rate was 5%.  Many blame the drought  – the fourth year of drought.  I have blamed poor water management and the weakening of water quality standards prescribed to protect the salmon (see previous posts).

It is now time for extreme actions to save these fish.  This coming year’s winter adult run will be made up primarily of the 2013 spawn, with some from 2012.  These spawns were marginally successful and could produce enough spawners next summer to help fix this debacle.

The responsible agencies plan to take more eggs and increase smolt production at the Livingston Stone Hatchery near Redding.  They also plan to truck these hatchery smolts to the Bay to maximize their survival.  They will likely severely limit commercial and recreational fisheries that may harvest Winter Run.  They plan to again start raising a rescue population in captivity to ensure they have some fish in the future to draw on for recovery.  A new drought plan will again address how flows and water temperatures will be managed below Shasta.  The State Board may resist weakening Sacramento River and Delta water quality standards designed to protect Winter Run, unlike what they did in the last two years.  All of these actions together will indeed help Winter Run from further decline, but it will not be enough even if the El Niño brings abundant rain and snow.

What else?  The answer to that question should be everything that is reasonably possible to increase production and survival.  Here are some suggestions:

  1. Do not weaken Sacramento River and Delta water quality standards that protect Winter Run. (This alone would have averted the catastrophes below Shasta the past two years.)
  2. Minimize warm water inputs to the Sacramento River in summer from the Trinity River to keep Sacramento River temperatures lower and save Shasta’s cold-water pool.
  3. Alter peaking hydropower management and system infrastructure in Shasta-Trinity CVP system to improve water temperatures in the Sacramento River and the conservation of reservoir cold-water pools.
  4. Further limit Shasta-Trinity reservoir releases to water contractors to conserve cold-water pools and maintain flow requirements for salmon.
  5. Enhance natural winter and spring flow pulses from tributaries below Shasta with flow releases from Shasta to increase survival of emigrating wild juvenile salmon migrating downstream in the Sacramento River, to and through the Delta, and to and through the Bay to the ocean.
  6. Conduct an aggressive rescue program of adult Winter Run that migrate into Sacramento Valley bypasses only to be blocked below overflow weirs, or that migrate into dead-end basins, or that stray into other tributaries including Battle Creek, Feather River, and American River salmon hatcheries.
  7. Capture wild juvenile Winter Run in an enhanced trapping program at fish screen bypasses, screw traps, and other techniques in the Sacramento River in fall and winter migration period, and transport these juveniles to the Bay to avoid lower river and Delta sources of mortality.
  8. Modify Delta operations to maximize juvenile Winter Run survival through the Delta. This may involve further changes to Delta Cross Channel operations and Delta export schedules, as well as Delta inflow and outflow.
  9. Maximize egg taking and rearing capacity in hatchery system.
  10. Barge wild and hatchery young from the Sacramento River through the Delta for release in the Bay to avoid future straying problems associated with trucking fish.
  11. Raise juvenile hatchery salmon in floodplain habitats in winter in the Sacramento Valley (e.g., Sutter and Yolo Bypasses).
  12. Conduct egg injection or fry releases in appropriate locations in Battle Creek to jumpstart its prescribed new population; this can be managed at the Battle Creek hatchery.
  13. Develop and implement an emergency comprehensive plan with appropriate agencies with the necessary authority to carry out these actions. Include stakeholders in the plan development and review process.  Obtain necessary funding from available sources.