Category Archives: Fish (general)

NMFS on Salmon and the Drought, Part 2

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As noted in the first blog of this series, 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.

April 8, 2014 Drought Operations Plan

On April 8, 2014, the Bureau and DWR issued a 2014 Drought Operations Plan, in which they proposed low releases in the Sacramento River in April and May:

Keswick releases will be held to no greater than 3,250 cfs, or as determined necessary to reasonably target no more than 4,000 cfs at Wilkins Slough, unless necessary to meet nondiscretionary obligations or legal requirements;

The critical phrase here is “nondiscretionary obligations.” It is the view of NMFS, as described in its Biological Opinion for the Operation of the State Water Project and Central Valley Project, that the Bureau of Reclamation does not have the discretion to release less water to Sacramento River Settlement Contractors than 75% of contracted amounts. Thus, low April and May flows called for in the 2014 Drought Operations Plan were overwhelmed by calls for water by the Settlement Contractors.

April 8, 2014 NMFS Letter on Sacramento River Water Temperature Management

On April 8, 2014, NMFS wrote a letter1 to the Bureau and DWR in response to their April 8, 2014 Drought Operations Plan. In that letter, NMFS concurred with the Plan, but highlighted a concern regarding deliveries to the Settlement Contractors:

“Winter-run Chinook salmon viability and Sacramento Settlement Contractor deliveries: Reclamation is working with Sacramento River Settlement Contractors on options to shift a significant portion of their diversions this year out of the April and May period and into the time frame where Keswick releases are higher to achieve temperature objectives on the upper Sacramento River. The willingness and cooperation of the settlement contractors in this effort would allow a modified diversion pattern and create the benefit of increased Shasta Reservoir storage at the beginning of the temperature control operations and increased availability of water to these senior water rights holders in this critically-dry year. This deferral of irrigation would allow implementation closer to the lower range of the Keswick release schedule for April and May, as identified in Section V of the DOP (Drought Operations Plan).

Thus the agencies and the Settlement Contractors were left to work out on a voluntary basis a mechanism to keep enough cold water in Lake Shasta to protect Winter Run salmon throughout the summer and fall. The State Water Board approved the Plan.

It didn’t work. Though releases from Shasta in April, 2014 were low, the Bureau ramped up releases from Shasta to the Settlement Contractors in early May (Figures 1 and 2), and cold water in Lake Shasta was depleted by the end of August.

Graph of May 2014 releases from Keswick

Figure 1. May 2014 releases from Keswick to the Settlement Contractors were far above those advised by NMFS (

Graph of releases May 2014

Figure 2. May 2014 releases from Keswick to the Sacramento River were diverted by Settlement Contractors upstream of the Delta. Contrast flow at Wilkins Slough (~25 miles north of Woodland) with releases from Keswick in Figure 1: most flow increases over the month were diverted north of the Delta.

January 29, 2015 Letter on Sacramento River Water Temperature Management

On January 29, 2015, NMFS wrote a letter to the Bureau and DWR in response to a new January Temporary Urgency Change Petition (TUCP) to the State Board.2 In its January 29, 2015 letter, NMFS’s acknowledged lessons from 2014 regarding water temperature:

Temperature management is critical. Salmon rely on cold water, particularly during early life stages when fish are young and vulnerable. Shasta and Keswick dams block endangered winter-run Chinook from accessing their native cold water habitat in the Upper Sacramento and McCloud Rivers, so their eggs and fry are particularly vulnerable to high summer temperatures. Data from the Sacramento River indicate 2014 temperatures were at levels that impact the survival of juvenile salmon and steelhead. We found that the 2014 temperature criterion was exceeded starting in August, resulting in approximately 95% mortality of eggs and fry upstream of Red Bluff Diversion Dam. As of December 16, 2014, an estimated 390,000 juvenile winter-run Chinook salmon passed Red Bluff, compared to 1.8 million in the previous brood year and 850,000 in brood year 2011, the year of the winter-run collapse (see Nov. 18 USFWS/CDFW/NOAA Fisheries presentation to State Water Board). This is the fewest winter-run Chinook juveniles per female spawner passing Red Bluff in 11 years.

March 27, 2015 Letter

However, by the end of March, 2015, NMFS was once again tiptoeing through a proposal by the Bureau to repeat the previous year’s disaster. On March 27, 2015 NMFS once again concurred with the proposed TUCP, even while highlighting the “conflict” between Winter Run salmon and deliveries to the Settlement Contractors. 3

The Project Description meets all of the required aspects of the contingency plan required in Action I.2.3 .C, as follows:

  • Reclamation has provided an assessment of additional technological or operational measures that can increase the ability to manage the cold water pool.
  • Reclamation notified the State Board, through filing the TUC Petition, that meeting the biological needs of winter-run and the needs of resident species in the Delta, delivery of water to nondiscretionary Sacramento Settlement Contractors, and Delta outflow requirements per D-1641 , may be in conflict in the coming season.
  • In conclusion, NMFS concurs that Reclamation’s Project Description is consistent with Action I.2.3.C and meets the specified criteria for a contingency plan. … Furthermore, the best available scientific and commercial data indicate that implementation of the interim contingency plan will not exceed levels of take anticipated for implementation of the RPA specified in the CVP/SWP Opinion.

And once again in 2015, no one stepped up to maintain cold water in Shasta Reservoir in April and May (Figure 3).

Graph of 2015 releases

Figure 3. In 2015, releases to the Settlement Contractors ramped up in April and were high throughout May.

July 1 Letter4

By July 1, 2015, NMFS was already issuing a post-mortem.

“NMFS acknowledges that storage in Shasta Reservoir at the beginning of the temperature management season in June, and the quantity and quality of the cold water pool, will not provide for suitable winter-run habitat needs throughout their egg and alevin incubation and fry rearing periods.”

Final Comment

We should expect more from the federal agency mandated to protect our endangered salmon. At a minimum, NMFS should have not concurred, in 2015 (or in 2014, for that matter), and should have called out the fact that added take of Winter Run would occur, further jeopardizing the viability of the species through direct mortality and degradation of their critical habitat.

Regardless of the legal merit of NMFS’s position that it does not have authority under the Endangered Act to limit deliveries to the Settlement Contractors, its failure to defend listed Winter Run gave cover to the Agency that has that authority: the State Water Board. CSPA, the Bay Institute and others asked the State Water Board in February, 2015 and again in the spring to reduce 2015 deliveries to the Sacramento Valley Settlement Contractors to save the Winter Run (and to protect Delta smelt). In an Order denying Petitions for Reconsideration of the 2015 TUCP’s filed by CSPA and others, the State Water Board offered the rationale:

However, at the time the changes were approved, the tradeoff appeared to be reasonable based on the information available at the time, including biological reviews from DWR and Reclamation and concurrence from the National Marine Fisheries Service (NMFS), U.S. Fish and Wildlife Service (USFWS), and California Department of Fish and Wildlife (DFW) (collectively fisheries agencies) with the changes. For these reasons, the petitions for reconsideration of the past Executive Director actions are denied. 5

NMFS on Salmon and the Drought, Part 1

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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 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)

Graph of Occurrence of juvenile salmon

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 )

Scott River – Crisis Update

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In a recent post1 I related that the Scott River, a major salmon producing Klamath tributary in northern California near Yreka and Fort Jones, is again in crisis due to low fall flows in the present drought. I suggested that normal December storms might be too late to save the Fall Run Chinook, but would likely accommodate the later spawning Coho.

Two December storms (Figure 1) have come and helped the salmon. Counts near Fort Jones recently reached near 400 for Chinook and 200 for Coho. Neither number is good, but the Chinook number, though preliminary, is very low, as it should be several thousand or more. Waiting for several months to ascend the river to spawn has likely taken its toll on the Chinook. The storms were also nearly too late for Coho, but these circumstances are fairly normal for Coho.

Graph of December streamflow in Scott River below Fort Jones

Figure 1. December streamflow in Scott River below Fort Jones. (Source: CDEC)

The late storms made things very difficult for Chinook. In a recent newspaper article2 on the Scott, it was noted that late runs usually spawn in the lower river, downstream of the good spawning reaches. The lower river spawning grounds are subject to winter storm scouring. In the article, some sources blamed the low fall flows on agricultural groundwater pumping during the summer and fall, which lowered the water table in Scott Valley. Lack of summer snow storage in the adjacent mountain ranges was also a key factor.

But the article and its sources miss what my previous post suggested as a solution to the problem. Groundwater could have been pumped into the river in the Valley in substantial amounts in the fall using some of the irrigators’ idle pumps. A concerted pumping effort in October and November, for one to several weeks, could have gotten the Chinook up from the mouth into the Valley to the perennial flowing spawning tributaries and river reaches. The salmon could have spawned or have been ready to spawn when the rains did come.

The winter rains are already recharging the groundwater basin in the Scott Valley, so the costs of the effort in terms of next year’s water supply would have been minimal. The cost of electricity is minuscule in comparison with the loss of production of one of the Klamath’s most prolific salmon-producing tributaries.

Some Delta Smelt Back in the Delta

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The US Fish and Wildlife Service’s early winter survey1 recently detected the first adult Delta Smelt of the water year in the Delta at Jersey Point on the lower San Joaquin River (Figure 1). The number collected in the survey through December 15th is 3, compared to 26 for the same period last year. Their appearance is on schedule and likely related to the first storm flow of the winter (Figures 2 and 3), and the freshening of the Delta (Figure 4).

Table of Smelt Count

Figure 1. Catch of adult Delta Smelt in early warning survey at two lower San Joaquin River stations in December 2015.

Graph of Delta freshwater outflow in December 2015

Figure 2. Delta freshwater outflow in December 2015. (Source: CDEC)

Graph of Turbidity of water at Jersey Point in December 2015

Figure 3. Turbidity of water at Jersey Pt in December 2015. (Source: CDEC)

Graph of Salinity (EC) at Jersey Point in December 2015

Figure 4. Salinity (EC) at Jersey Pt in December 2015. (Source: CDEC)

More on Spill

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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.

Graph of flow spike

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.

Map of winter run spawning location

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.

Graph of catch index in Knights Landing

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

Graph flow from Keswick 2003

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.

Graph of trawls 2004

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

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