NMFS on Salmon and the Drought, Part 1

Posted on December 25, 2015 by Tom Cannon and Chris Shutes

The National Marine Fisheries Service (NMFS) is responsible under the Endangered Species Act for protecting the endangered Winter Run Chinook salmon of the Sacramento River. But when the US Bureau of Reclamation (USBR or Bureau) and the Department of Water Resources (DWR) have asked NMFS to comment on proposed changes in Central Valley Project operations during the present four-year drought, NMFS has consistently concurred, often going against its own previous prescriptions and advice. As a consequence, the Winter Run salmon were put at great risk, decimating the 2014 and 2015 year classes and again placing the population at the brink of extinction.

January 29, 2015 Letter on Old and Middle River Flows

On January 29, 2015, NMFS wrote a letter in response to the Bureau and DWR’s January Temporary Urgency Change Petition (TUCP) to the State Board.¹ The Petition asked the State Board to weaken State water quality standards. NMFS stated:

Here’s what we learned from monitoring salmon in 2014 that will inform our strategies for managing the drought in 2015:

1. Managing Old and Middle River (OMR) flow regimes to protect salmon is critically important. Effectively managing flow regimes allows juveniles to stay in the best habitat in the North Delta, ensuring they are not drawn toward the South Delta pumps where they are frequently killed by predators or the pumps themselves. During a rare rainstorm last March, and under a flexible operation approved as part of the 2014 Drought Contingency Plan, we allowed for higher levels of pumping and reverse OMR flows. Evaluating the effects of the action this fall, we learned that salvage and loss of juvenile Chinook salmon, including winter-run, at the federal and state fish collection facilities increased when OMR’s 14-day running average was more negative than -5,000 cfs. This confirms the importance of managing OMR flows carefully to ensure pumping is increased when it will be most effective for increasing water supply and least impactful to juvenile fish.

Regardless of whatever NMFS had learned from events in 2014, NMFS had already ignored these lessons in December 2014 when it allowed OMRs to significantly exceed the -5000 cfs limit (Figure 1). NMFS then acquiesced to high reverse flows in the 2015 Drought Operations Plan: “OMR shall be no more negative than -5,000 cfs as a 14-day running average, and no more negative than -6,250 cfs as a 5-day running average, except as needed to capture sporadic storms (increase exports).”

The first winter storms usually trigger emigration of juvenile Winter Run and Late Fall Run Chinook salmon into and through the Delta (Figure 2). The only time during a drought that operators can achieve the highly negative OMR levels is in sporadic storms. Since those are precisely the conditions under which emigrating salmon pass through the Delta, the highly negative OMR flows put migrating juvenile salmon at great risk.

Figure 1. Old and Middle River flows in December 2014. Negative or reverse flows are caused by South Delta Exports, which reached over 10,000 during the second week of December 2014. (Data source: CDEC)

Figure 2. Occurrence of juvenile salmon in winter 2004 in seines and trawls near Sacramento at entrance to tidal Delta. Other years have shown a similar pattern. (Source: http://www.science.calwater.ca.gov/pdf/ewa/ support_docs_110804/Salmon%20Criteria%20Figures%201_2_Chappell.pdf )

http://www.usbr.gov/mp/drought/docs/2015-01-29_NMFS_TUCP_response_letter.pdf ↩

More on Spill

Posted on December 15, 2015 by Tom Cannon

In a recent post I suggested “spill” (targeted reservoir releases) to enhance salmon production in Central Valley rivers. Well, it is now time to employ spill to help Winter Run and Spring Run Chinook salmon in the upper Sacramento River below Shasta near Redding. Waiting for El Niño to help these fish may be too late. Confidence and early indications that El Niño will come this winter should make the necessary commitment for spill now more palatable. Spill releases could have already been made from Shasta Reservoir with these recent storms to support emigration of young salmon from the spawning and rearing reach.

After the salmon spawning, irrigation, and water transfer season ended in October, there have only been minimum flows and no spills to enhance young salmon emigration. Flow from Shasta-Keswick (river mile 302) has remained near the minimum requirement of 4000 cfs (Figure 1).

Recent Storms – December 2015

The recent storms have sharply increased flow in the Sacramento River downstream of the spawning reach at Bend Bridge at river mile 258 (Figure 2) below the input of four large creeks entering the Sacramento River below Redding (Figure 3). Inflow to Shasta Reservoir has nearly quadrupled during the two storms, reaching 8,000-10,000 cfs. A prescriptive “spill” release of 5-10% of inflow (500-1000 cfs) is needed. That would raise Keswick releases to about 5000 cfs, which would help stimulate emigration from the spawning reach into the higher flow reach below the tributaries, and down into and through the Delta.

December 2003 Case Study and Precedent

December 2003 had similar circumstances. Screw trap catch of Winter Run salmon at Knights Landing (RM 90) had a sharp increase coincident with flow increases in December 2003 (Figure 4). Spill in December 2003 (Figure 5) helped increase the river flow.

Concern for Young Salmon in the Delta

Higher freshwater inflows from the storms in 2015 have already pushed the Low Salinity Zone out of the Delta into Suisun Bay. Winter Run and Spring Run salmon (as well as Late Fall smolts and Fall Run fry) are likely now entering the Delta in large numbers (comparable monitoring results from 2003-4 are shown in Figure 6). Spill wouldl help move fish through the Delta and west to the Bay. The Delta Cross Channel remains open, allowing the emigrating salmon to spread into the Central Delta. This increases the need for spill to keep these fish moving west before the DCC is closed and south Delta exports divert freshwater inflow and emigrating salmon away from the Bay and toward the Delta pumps.

Spill is also needed from other reservoirs on the Feather, Yuba, and American Rivers that have also received significant inflow during the recent storms. Spill from these reservoirs is needed to stimulate migration of young salmon from their tailwaters as well as to contribute more to the combined Delta inflow and outflow.

Though it is a hard decision not to store all of the inflow from these first storms of the season in reservoirs, releasing 5-10% as spill would go a long way to help saving the wild endangered salmon that depend on the early winter flows.

Graph of releases from Keswick fall 2015

Figure 1. Flow releases to Sacramento River from Keswick Reservoir fall 2015. Minimum prescribed outflow to Sacramento River is approximately 4000 cfs in drought years like 2015. Keswick Dam is at rivermile 302, nine miles below Shasta Dam.

Figure 2. Flow in the Sacramento River at Bend Bridge (RM 258) 44 miles below Keswick Dam fall 2015. Flow spikes from recent storms come from local tributary creeks upstream of Bend Bridge.

Figure 3. Location of Winter Run spawning and rearing reach (green hatched line) below Keswick Dam (RM 302) near Redding, CA. Four major tributary creek inputs are shown below Redding. The mouths of Cottonwood and Battle Creeks are about RM 270.

Figure 4. Catch index of older juvenile (non-fry) in Knights Landing (RM 90) rotary screw trap Oct 2003-Mar 2004. Source: http://www.science.calwater.ca.gov/pdf/ewa /support_docs_110804/Salmon%20Criteria%20Figures%201_2_Chappell.pdf

Figure 5. Flow releases to Sacramento River from Keswick Reservoir fall 2003. Releases were approximately doubled to 9000 cfs at mid-month, ostensibly to help stimulate young salmon emigration and allow greater Delta exports ¹.

Figure 6. Catch index of older juvenile (non-fry) in trawls and seines in the Sacramento River near Sacramento, Oct 2003-Mar 2004. Source: http://www.science.calwater.ca.gov/pdf/ewa /support_docs_110804/Salmon%20Criteria%20Figures%201_2_Chappell.pdf

High exports in December03-January04 did result in substantial counts of juvenile Winter Run salmon at South Delta Fish Salvage Facilities during the period. ↩

Spill and Salmon Survival

Posted on December 13, 2015 by Tom Cannon

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.

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.

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

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.

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.

Figure 6. Shasta Reservoir inflow in water year 2015.

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

Salmon Drought Plan – there is no plan

Posted on November 24, 2015 by Tom Cannon

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

Posted on November 22, 2015 by Tom Cannon

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.

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.

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.
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.
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.
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.
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 .

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