Lake Shasta and Sacramento River Operations: Lessons Learned – #1, Part 2

Following an introductory post, this is the second post in a series on the lessons learned by the National Marine Fisheries Service (NMFS) from the 2013-2015 drought that devastated Sacramento River salmon populations.  The first post addressed Lesson #1 and its non-application in the first half of 2020. 

This post addresses how the non-application of Lesson #1 in 2020 evolved into a tug-of-war in the second half of 2020 and has cascaded into non-action so far in 2021. For more detail and links, see CSPA’s March 15, 2021 letter to the State Water Board urging immediate action to protect Sacramento River and Delta fisheries in 2021.  See also the State Water Board’s Sacramento River Temperature web page, though some of the links are not live, at:

Water and fisheries managers have known for many years that both the Lake Shasta storage level on April 1 and spring releases from Shasta determine how much cold water will be available in the lower Sacramento River through the summer.  However, in 2020, as discussed in Part 1 of this series, the Bureau of Reclamation (Reclamation) refused to decide on water temperature management options for Shasta Reservoir and the lower Sacramento River before April 1.  Reclamation submitted a draft temperature management plan (TMP) to the State Water Board on April 23 and a final TMP on May 20, neither of which evaluated reduced delivery options whose analysis the State Water Board had requested.

Meanwhile, Reclamation was operating in 2020 in the first year of the new Trump-era Biological Opinions for the long-term operation of the Central Valley Project (CVP) and the State Water Project (SWP).1 The stated purpose of these Opinions was to “maximize deliveries” of water to contractors, and did they ever deliver.  See part of the results in Figure 4 of the previous post: very high deliveries to Sacramento River CVP contractors in April and May, so that water in Lake Shasta was committed before the plan to operate Shasta was complete.

By June 1, 2020, the State Water Board had rejected Reclamation’s TMP.  In its June 1, 2020 letter refusing Reclamation’s May 20 TMP, the State Water Board wrote:

Reclamation has declined to evaluate additional operational scenarios. Reclamation’s position is that scenarios with different operational assumptions would be inconsistent with its contractual obligations, and are therefore beyond Reclamation’s reasonable control. The State Water Board disagrees. To the extent that Reclamation delivers water under its own water rights, Reclamation’s obligation to deliver water to its contractors does not take precedence over its permit obligations.

On July 17, 2020, CSPA and its partners reached a settlement agreement with the State Water Board that dealt in substantial part with Sacramento River temperature management.  The settlement agreement requires the State Board to conduct a transparent Sacramento River Temperature Management process.  The process must address all controllable factors, including deliveries, and ensure adequate staffing, modeling and public review.  The CSPA settlement became part of the dispute between Reclamation and the State Water Board in the following months.

After exchanges of letters between Reclamation and the State Water Board in June and July, and an addendum to the TMP on July 31, the State Water Board gave up on 2020 and in an August 4 letter  tentatively approved the TMP, subject to conditions, two of which stated:

  • Reclamation shall develop a draft protocol by September 30, 2020, that meets the criteria identified by the State Water Board;
  • By September 15, 2020, Reclamation shall provide additional information concerning fall operations, including the volume and timing of releases and deliveries each month through December.

On August 31, the State Water Board sent a follow-up letter clarifying its request of Reclamation:

As part of the State Water Board’s conditional approval of Reclamation’s 2020 Temperature Management Plan (TMP), Reclamation is required to develop an initial draft protocol by September 30, 2020. The State Water Board will hold a public workshop this fall in coordination with Reclamation to receive public comment on the initial draft protocol to inform its completion. Once public comments are received, the Board intends to work with Reclamation to refine and finalize the protocol before the beginning of the next temperature planning and water supply allocation season in February 2021. The Board has requested that the protocol include the elements specified in the settlement agreement with the California Sportfishing Protection Alliance, et al., which the Board recently forwarded to Reclamation. This letter provides additional detail regarding issues that should be addressed as part of the protocol.

None of it happened.  No protocol.  No public workshop.  No public comments.  No disclosure to the State Water Board of the timing and releases of release and deliveries from September through December.  No final protocol by February 2021.  Instead, one final letter from Reclamation on September 30, deflecting the issue to the settlement with CSPA even though the issues in the settlement were issues raised by the State Water Board months before the settlement was completed: “Reclamation does not consider a state court voluntary settlement, to which Reclamation is not a party, as valid, enforceable legal requirements imposed on Reclamation.”

After all the correspondence, Reclamation affirmed on September 30 that it was right the first time: “The process for analyzing conditions and incorporating the best information into water management decisions for temperature management at Shasta Reservoir is outlined in the Shasta Cold Water Pool Management Flow Guidance document which was shared with the State Board staff on April 2, 2020.”

And so it comes full circle.  Faced with adversity last fall, the State Water to date performed as it all too often has: it has done nothing.  The Ides of March have passed, and there is every sign that the State Water Board will for a second straight year allow Reclamation to once again defy Lesson #1: Keswick releases need to be decided by April 15.

Sacramento River Salmon Redd Dewatering in Fall 2020

The Bureau of Reclamation’s standard fall operation of Shasta Reservoir and Keswick Reservoir dewaters the redds of fall-run Chinook salmon in the upper Sacramento River near Redding.  The peak in fall-run Chinook salmon spawning is October-November.  Eggs and alevin (hatched sac fry) remain buried one to two feet down in the gravel spawning bed (redd) for about three months.  As I described in a November 2019 post and in prior posts, drops in flow and associated water levels cause varying degrees of redd stranding or dewatering, and the affected eggs and alevins die.

Fall-run salmon spawn from September to December, with a peak in October-November.  It takes several months for eggs to hatch and fry to leave the gravel beds.  Under unregulated conditions, fall-run salmon spawn in the generally stable flows of fall, and their young move toward the ocean with winter rains.  The natural versus present managed flow patterns are compared in Figure 1.

The problem has been getting worse in recent decades with the greater emphasis on water deliveries and on summer spawning conditions for winter-run salmon.  Each fall, after the summer irrigation and the incubation period for winter-run Chinook salmon wind down, Reclamation reduces reservoir releases from Shasta and Keswick by 20-30%, especially in drier years like 2020 (Figure 2).  Water levels in 2020 dropped about 3 ft over the fall (Figure 3), completely dewatering the earliest redds.

Reclamation should have averted the problem by maintaining fall releases from Shasta near 5000 cfs (Figure 3), at a cost of about 100,000 acre-ft of Shasta storage for the fall, or about 5% of Shasta dry-year minimum storage (Figure 4).  The need would continue into early winter, but the effect on Shasta storage would depend on winter precipitation.

Figure 1. Managed vs full natural flow from Keswick Dam to the upper Sacramento River in fall 2020.

Figure 2. Keswick Dam water releases in 2020 and 57-year average.

Figure 3. Water levels in Sacramento River below Keswick Dam in 2020.

Figure 4. Shasta Reservoir storage in 2020. Note the reservoir had 1.3 million acre-ft of additional water stored at the beginning of the year than at the end. Water year 2019 was wet and 2020 was dry.


Scott River Chinook Salmon Update

The Scott River Chinook salmon, a key contributor to the overall Klamath River salmon run, are in major trouble.  In a November post, I had a “mixed” prognosis for this year’s fall run.  Well the numbers are now in – a record low, bleak run of 117 spawners observed (Figure 1) at the weir downstream of Fort Jones.

Figure 1. Scott River fall run salmon escapement 1978-2020. Source: CDFW unpublished data.

The poor run can be directly attributed to lack of fall river flow, a fact that I had addressed in a 2017 post.  Salmon simply cannot ascend the lower Scott River into Scott Valley spawning grounds from the Klamath River because of lack of streamflow.  Some may spawn in the steep canyon below the Valley (and counting weir), but poor spawning habitat and low flows in the canyon offer little solace for the salmon.

Poor fall flows (Figure 2) can be directly attributed to fall groundwater extraction and surface water diversions for hay-pasture irrigation.  The State Water Board should stop crop irrigation after October 1.  This irrigation practice has been getting worse over the past several decades, aided by improved well extraction and sprinkler technology and greater demand and higher revenues.  Present water use permits allow irrigation into December, which ranchers have been taking advantage of to get an extra crop of hay (with the help of climate change).

Unlike 2020 (Figure 2), water use in past drought years tapered off earlier and flows increased during October (Figures 3-5).  This allowed fall-run salmon access to the Valley.  In contrast, recent wet and normal years see a combination of precipitation and reduced water use, which enhances fall flows (Figures 6 and 7).

In conclusion, the State Board should limit fall water irrigation in Scott Valley to save the salmon.  The Sustainable Groundwater Management Act (SGMA), passed in September 2014, requires local agencies to develop Groundwater Sustainability Plans (GSP) that will assess and project future groundwater conditions, and provide management and monitoring activities.  The Scott River basin is a priority basin.  Siskiyou County is required to develop and submit a GSP for the Scott River basin by January 31, 2022.  A preliminary plan recently developed by the advisory group suggests reducing irrigation acreage (Figure 8) to increase streamflow (Figure 9).  That would help, but what salmon need is a cutoff of irrigation by October 1.  An option for further augmentation is to employ unused groundwater extraction wells in the fall to add water to the river  for short periods.  Stored water in the tailings ponds (red area in Figure 8) could also be gravity-fed or pumped into the river at critical times.

Figure 2. Scott River flow fall 2020. Water year 2000 was a drought year.

Figure 3. Scott River flow fall 2000 and winter-spring 2001. Water year 2001 was a drought year.

Figure 4. Scott River flow fall 2013 and winter-spring 2014. Water year 2014 was a dry year.

Figure 5. Scott River flow fall 2014 and winter-spring 2015. Water year 2015 was a normal year.

Figure 6. Scott River flow fall 2016 and winter-spring 2017. Water year 2017 was a wet year.

Figure 7. Scott River flow fall 2017 and winter-spring 2018. Water year 2018 was a below normal water year.

Figure 8. Baseline (present) and preliminary action alternative for Scott Valley irrigation. Source: preliminary plan.

Figure 9. Analysis of preliminary action alternative. Source: preliminary plan.



Yuba River Salmon 2020

In a 2017 post and a 2018 post, I related the status of Yuba River Chinook salmon runs. The 2017 spawning escapement estimate was a record low. The 2018 and 2019 runs were not much better (Figure 1). While the record low 2017 can be blamed predominately on the 2013-2015 drought, the poor 2018 and 2019 runs cannot. Water year 2016 was a normal water year and 2017 was a wet year.

The likely culprit in the decline in Yuba escapement is the continuing persistent decline of wild spawners and increase in hatchery strays (greater than 90% of the run), leading to the erosion of the locally adapted Yuba River salmon population. This was the diagnosis for the overall Feather River population by Willmes et al., 2018.

Figure 1. Yuba River fall run salmon escapement 1953-2019.

A further look at the composition of the hatchery strays in the Yuba escapement surveys provides added clues about the cause of the recent decline in overall escapement to the Yuba River. In 2016 (Figure 2), nearly half the tag returns were strays from the Battle Creek hatchery, while the other half were a combination of spring-run and fall-run strays from the Feather River hatchery, along with a smattering of strays from the hatcheries on the American and Mokelumne rivers. In 2017 (Figure 3), Yuba tag returns featured an even greater proportion of strays from Battle Creek, the American, and the Mokelumne. In 2018 (Figure 4), about half of the tag returns were from the Mokelumne River hatchery, and a third were of Feather River spring-run hatchery origin.

Feather-tagged spring-run show up consistently in the Yuba escapement surveys. This is unusual, because spring-run make up only about 10% of the Feather hatchery smolt production, with fall-run being about 90%. One reason is that spring-run smolts are 100% tagged, while fall-run hatchery smolts are only 25% tagged. Another reason is that all the spring-run smolts are released near Gridley just upstream from the mouth of the Yuba, whereas most of the fall-run smolts are released in the Bay. A third reason is that in most years springtime flows in the Yuba are higher and colder than those in the Feather, and are thus more likely to attract returning adults. Regardless of the reason, the fact that a significant portion of Yuba “fall run” escapement is derived from spring-run hatchery smolts is cause for concern.

Battle Creek hatchery fall-run made up about half the tag returns in 2016 and 2017. Much of the smolt production from the Battle Creek hatchery was trucked to the upper Bay in 2014 and 2015, a strategy prone to increased straying.1 No Battle Creek hatchery smolts were trucked to the Bay in 2016, and none showed in the Yuba in 2018. With over 10 million fall-run smolts produced at the Battle Creek hatchery (federal Coleman Hatchery near Red Bluff), nearly double the Feather hatchery production, it is easy to see why Battle Creek hatchery salmon could dominate the Yuba escapement. Without the Battle Creek, American River, and Mokelumne River hatchery strays in 2017, the record low escapement in the Yuba River would have been far worse. The fact that most of the 2017 spawners were hatchery strays from rivers other than the Feather should also be cause for concern.

In conclusion, the escapement of fall-run salmon to the Yuba River has declined over the past five years, approaching record-low levels. Spawners are now predominately hatchery strays from smolts released in the Bay and along the coast. Natural “wild” Yuba River smolt production is virtually nonexistent. This is a crying shame for what is widely regarded as one of the best non-hatchery salmon rivers in the Central Valley. I have spent many days on the Yuba River over the past two decades. I observed the big runs at the turn of the century and in 2013 and 2014. The river’s pools turned purple with adult salmon. Dead and dying salmon filled the backwaters, feeding eagles and buzzards. The odor was prevalent. Spawning salmon and redds were everywhere. Such occurrences are now rare. Our Yuba River needs so many fixes, a subject for another post.

Figure 2. Composition of tag returns from Yuba River spawners in 2016. FRS = Feather River spring run. MRF = Mokelumne River fall run. FRF = Feather River fall run. ARF = American River fall run. BCF = Battle Creek fall run. MeRF = Merced River fall run. Data source:

Figure 3. Composition of tag returns from Yuba River spawners in 2017. FRS = Feather River spring run. MRF = Mokelumne River fall run. FRF = Feather River fall run. ARF = American River fall run. BCF = Battle Creek fall run. Data source:

Figure 4. Composition of tag returns from Yuba River spawners in 2018. FRS = Feather River spring run. MRF = Mokelumne River fall run. FRF = Feather River fall run. ARF = American River fall run. Data source:

Klamath’s Shasta and Scott Rivers – Update Fall 2020

In a November 2019 post, I gave updates through 2018 on the status of fall-run salmon in the Scott and Shasta rivers, major tributaries of the Klamath. I described how continuing improvements in river management paid off for the Shasta River’s fall Chinook run. I also described how lack of protections in water management left the Scott run in poor condition.

In this post, I update fall-run Chinook spawning escapement through 2019, with some insight into the 2020 runs. I also provide data on the runs in the Salmon River, the Scott and Shasta’s sister Klamath tributary. The 2019 salmon runs should have benefitted from water-abundant 2017, but may have been handicapped by poor numbers of returning spawners in 2016.

The runs of fall-run Chinook in all three of these major Klamath River tributaries improved in 2019 compared to the runs in 2016 that were severely affected by drought and fire.1 However, runs in all three rivers in 2019 fell short of the 2017 and 2018 runs (Figure 1). Good water conditions in all three rivers in 2017 (Figure 2)2 should have led to improvements in runs over 2017, which were a product of 2014-2015 drought and 2014 fires. They also should have been better than the runs in 2018, whose runs were spawned in drought year 2015 and reared in dry year 2016.

The fact that there was not greater improvement in the 2019 runs is likely the consequence of low numbers of spawners in the fall of 2016. The low number of spawners in 2016 resulted from the continuing effect of the devastating 2014 fires on the watersheds (especially the Salmon River), ongoing poor water management (especially in Scott and Shasta rivers), and poor water conditions in the dry falls of 2017 and 2018 (limiting 2019 the returns of 2-year-old “jacks and jills”).

The prognosis for 2020 is mixed. This results on the upside from improved numbers of spawners in 2017 and a wet water year in 2019. On the downside, the relatively poor water conditions in fall 2017 and the dry conditions in 2018 and 2020 are likely to depress the numbers of adults that return in 2020. Initial counts from Shasta and Scott rivers3 however indicate poor runs not unlike 2004 or 2016. Overall, the decline in spawners produced from strong runs (2014 and 2017) in the Klamath’s main wild salmon tributaries, as well as drought, fire, and continuing poor water management, do not bode well for the future of Klamath salmon.

Figure 1. Shasta, Scott, and Salmon River escapement of fall-run Chinook salmon 1978-2019. Source; CDFW data.

Figure 2. Salmon River streamflow 2013-2020 with long-term average.