Category Archives: Chinook Salmon

Sacramento River Fall Run Chinook Salmon – 2020 Update

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When I last updated the status of the mainstem Sacramento River fall-run salmon below Shasta in a July 2019 post, I expected 2019 in-river escapement to improve from the 2017 record low run (Figure 1). The record low 2017 run had been the consequence of extreme drought conditions during 2015, the third year of a major drought. In contrast, the 2019 run was largely the progeny of water year 2017, a wet year with good spawning, rearing, and migrating conditions for the 2016 salmon brood year. A potential negative ingredient to the 2019 escapement was the poor number of spawners returning in the fall of 2016 that spawned brood year 2016 (Figure 2). Likewise, 2020 escapement ingredients included the record low number of spawners in 2017, as well as poor rearing and migrating conditions in winter-spring of below-normal water year 2018.

In an April 2017 post, I presented the status of the overall fall-run salmon for the Sacramento River basin that included escapement to the mainstem, tributaries, and hatcheries. Updates of those numbers are shown in Figure 3. The total river escapement, like the upper Sacramento in-river escapement, was depressed from 2015 through 2018. Escapement in 2019 improved, but it declined again in 2020. The 2019 and 2020 Sacramento salmon runs were improved over the 2015-2018 drought-influenced runs, but were lower that returns from other wetter years, because their parental spawner numbers were depressed in 2016 and 2017 (Figure 4). Note in Figure 4 the 2019 run is shown by blue-17 to represent the wet year rearing and emigrating conditions for the 2019 run. The figure depicts the positive spawner-recruit relationship and the strong water-year type influence from two years earlier on the adult escapement (run size).

The prognosis for the 2021 and future runs is poor because of the low number of spawners in recent years and drier water year winter conditions in 2018, 2020, and 2021. Restrictions on the 2021 fishery are likely1 despite wet year 2019 conditions. Hopefully, the 2021 run will show improvement with the restricted fishery and better production from wet year 2019.

Figure 1. Fall-run Chinook salmon escapement (run size) in the mainstem in-river Sacramento River 1978-2019. Source: https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=84381

Figure 2. Spawner-Recruit relationship for upper Sacramento River mainstem fall run Chinook salmon. Number is recruitment year (escapement). Spawners are recruits from three years prior. Numbers are log minus 3 transformed. Red is for dry water year two years prior during rearing and emigration. Blue is for wet year. Green is for normal water year. For example: red 17 represents 2017 run that reared in drought year 2015, with spawners (parents) being 2014 run green number.

Figure 4. Sacramento River spawners versus recruits three years later from escapement estimates (Log10X – 4 transformed). Note that some variability likely occurs from a low number of 2- and 4-year-old spawners in the escapement estimates. Numbers are sum of hatchery, mainstem, and tributary estimates from CDFW GrandTab database. Number shown is rearing year (winter-spring) following fall spawning year. For example: “88” represents rearing year for 1987 spawning or brood year. These fish returned to spawn (recruits) in 1990. The red “07” represents the record low run in fall 2009. Red years are critical or dry water years. Blue years are wet water years. Green years are normal water years. Red circles represent adult return years being drier water years. Blue circles represent return years being wet water years. Green circles represent return years being normal water years. Orange square denotes outlier years influenced poor ocean conditions, floods, or hatchery management factors. Note that runs from wet years are up to ten times higher (1 log number) than the drought influenced years, particularly 87-90, 07-08, and 12-15.

 

 

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

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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: https://www.waterboards.ca.gov/waterrights/water_issues/programs/drought/sacramento_river/index.html

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.

Lessons Learned from the 2013-2015 Drought

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After the 2013-2015 drought, the National Marine Fisheries Service (NMFS) took a deep dive into “lessons learned” to help guide future regulatory permit processes, especially those that address the effects of future Shasta Reservoir operations on endangered winter-run Chinook salmon.  The drought proved to be a comprehensive adaptive management experiment on the effects of the US Bureau of Reclamation’s (Reclamation) operation of its Shasta-Trinity Division on Sacramento River and Bay-Delta fish populations.  Though the specific lessons learned focused primarily on one listed species, winter-run salmon, the effects manifested in different ways on other listed or special-status native fish species in the Central Valley and Klamath-Trinity rivers, including other runs of salmon, steelhead, sturgeon, and smelt, and even orca in the ocean.

In upcoming posts, I will discuss the ramifications of the “lessons” and their relevance to fish populations and water supply issues.  The focus will be on Sacramento Valley salmon and how Reclamation can adjust the operations of the Shasta-Trinity Division to help salmon and other fish populations recover.

March 2021 is a critical stage of decision making in managing resource allocation during what could be another dry year like water year 2020.  Reservoir storage levels are low (Figures 1-3), and Shasta’s cold-water supply (Figure 4) is low after a dry year.  Water year 2021 is dry so far.  The lessons learned need to be applied to avoid the fisheries disasters of the last drought.  Will the warnings and lessons be heeded?

Figure 1. Shasta Reservoir water storage for water years 2018-2021. Note reservoir refilled in wet year 2019 but not in below normal 2020, and storage enters 2021 at a low level.

Figure 2. Folsom Reservoir water storage for water years 2018-2021. Note storage entered water years 2020 and 2021 at lower levels, which does not bode well if water year 2021 is dry.

Figure 3. Oroville Reservoir water storage for water years 2018-2021. Note reservoir storage was poor after wet water year 2017 because of 2017 spillway failure.

Figure 4. Shasta Reservoir cold-water pool supply in calendar years 2014-16, 19, and 21. Note 2021 (black line) is beginning to trend toward drier year levels.

Water year 2021 is a bad year for American River wild salmon and steelhead production.

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Water year 2021 has been bad for American River salmon and steelhead, with very low Folsom Reservoir releases Oct-Jan (Figure 1a).  Water year 2021 can best be described as a dry year, at least through the first quarter, somewhat on the drier side of 2018 and 2020, which were below normal water years.  However, whereas 2018 and 2020 followed wet years, water year 2021 follows a drier year.  This means 2021 started with poorer Folsom Reservoir storage (Figure 1b).

Water year 2021’s low fall and early winter reservoir releases from Folsom were nearer to 1000 cfs than the normal 2000 cfs.  As a result, much of the good spawning and early rearing fry habitat in the river below the dams remained dry (Figure 2).  In contrast, even in drought year 2014, the side channel spawning habitat remained slightly watered at 600 cfs river flow (Figure 3).  So, not only are redds dewatering in early winter of these dry years, the dewatering or drying of the side channels is getting worse.  This is either because the main channel is incising from persistent scouring or because sediment deposition blocks the entrance to the side channels, leaving perched side channels high and dry.

What got us into this predicament?  Was it simply Mother Nature or global warming?  Water management should take part of the blame (Figures 4 and 5).  The end-of-September Folsom storage in 2019 was higher than average at 700 TAF after a wet year.  Flood control rules required reservoir levels to be down to 600 TAF in November.  But storage dropped to 500 TAF, with higher-than-normal fall releases (Figure 6), essentially shorting the reservoir 100 TAF in the new 2020 water year.

The American River Water Forum Agreement Is designed to manage and protect all water users, including salmon.  Its formula for reservoir releases is based on natural flow input levels to the reservoir for that water year, which was lower than normal in 2020, thus leading to the prescribed low fall 2020 reservoir releases.  With reduced storage and low reservoir inflow in 2020, it was impractical to release the needed 2000 cfs for salmon and steelhead in fall 2020 without dropping the reservoir down to 200 TAF in what could be a drought year.

In conclusion, the American River salmon and steelhead are at the mercy of a precarious water management system that can go from good to bad in one water year.  One answer to this low fall flow problem is to ensure there is an extra 50-100 TAF of reservoir storage at the end of September to maintain the needed higher fall and winter flows for salmon and steelhead.  Because the channel morphology also continues to change, sediment supply and river morphology must also be taken into account, if not also adjusted.

Figure 1. Oct-Jan Folsom Reservoir releases 2017-2021 with long term average (above) and reservoir storage (below).

Figure 2. Sunrise side channel (looking upstream) end of January 2021 with some of the best spawning and rearing habitat for salmon and steelhead in the lower American River nearly dry with river flows at 1000 cfs. Other important side and main channel spawning and rearing habitats were similarly compromised. Note main channel is at extreme left middle of photo.

Figure 3. Sunrise side channel (looking downstream) on January 15, 2014. Some of the best spawning and rearing habitat for salmon and steelhead in the lower American River is in this side channel. In 2014 as shown, it was almost dry with river flows at 600 cfs. Note tops of salmon redds sticking out of the water in various stages of dewatering. The redds were dug by salmon earlier in fall 2013 at 1200 cfs.

Figure 4. Folsom Reservoir storage (acre-ft) in fall 2017-2020. Water years 2017 and 2019 were wet years, and water years 2018 and 2020 were below normal years.

Figure 5. Folsom Reservoir releases (cfs) in fall 2017-2020. Water years 2017 and 2019 were wet years, and water years 2018 and 2020 were below normal years.

Figure 6. Folsom Reservoir release (cfs) in fall 2019 with 64-year average.

Tisdale Weir Fish Passage Project

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The California Department of Water Resources (DWR) Division of Flood Management is planning a major fish passage improvement to the Sutter Bypass: a notch in the Tisdale Weir.1 The notch will extend and enhance river flows into the bypasses, thereby allowing more access for juvenile salmon to rear in the bypass and improved upstream adult salmon passage from the bypasses back into the Sacramento River. DWR plans to place an operable gate in the notch, which DWR would open when flows over the weir ceased. This would extend the duration of flows into the bypass. As planned, DWR would not open the gate until after the weir had already overflowed.

In a May 2019 post I described similar improvements to fish passage into and out of the Yolo Bypass, including notches in the Fremont Weir at the upstream end of the Yolo Bypass where high flows in the Sacramento River overflow into it.

Potential Benefits:

Improving adult upstream passage and expanding rearing access to the bypasses with notch flows is a good concept. Improving rearing habitat in the bypasses is a further potential benefit. In wet years and in even in drier years (when the bypasses receive no Sacramento River overflows (or young salmon) even from the new notches), there will new potential benefits to tributary salmon populations (e.g., salmon from Butte Creek and the Feather and Yuba rivers). Sacramento River hatcheries can also improve their contributions by out-planting fry salmon to wetlands in the bypass. Managed wetlands in the bypass (including duck clubs and rice fields) can also be used for rearing wild and hatchery fry salmon, especially in drier years.

Potential Drawbacks:

More flow and access to the bypasses has the potential to put more salmon in harm’s way. More of the populations will rear and migrate in the bypasses. Stranding and predation in the bypasses are very real risks to young and adult salmon. Such risks need to be minimized. Rearing habitats need to drain effectively. Stranded young and adults should be rescued to the extent reasonably possible. There is a tendency in project plans and operations to ignore or downplay the stranding risks.

Further Needs:

There are multiple Sacramento River flood-control weirs that at times overflow into the Sutter Bypass and Butte Basin. These other weirs also need “fixing.” However, stranding (poor draining) in Butte Basin and Sutter Bypass will remain a serious problem, because hundreds of square miles of poor habitat conditions occur from top to bottom. Drainage and stranding need to be addressed before more access is provided. Information on smolt survival and run contribution from bypass rearing and passage is largely lacking.

Further Options:

Often the first major flow pulses in the Sacramento River bring the strongest downstream movements of young salmon (Figure 1). Proposed operation of the Tisdale Weir calls for the new gates to remain closed until after the weir overflows (Figure 2). This operation does not take advantage of a significant potential project benefit. For instance, had the new facilities been in place during the peak early-January fry emigration in wet year 2019 (Figure 1), the weir gates would have remained closed (lower graph in Figure 2) when they could have been opened prior to weir overflow on about January 12. The gates could also be opened in earlier pulses and more frequently in drier years like 2018 (top graph in Figure 2). Furthermore, early openings in wet and dry years would accommodate access to floodplain habitats for juvenile winter-run salmon (Figure 3). DWR would need to develop some forecasting and decision-making protocols to evaluate opening the new gates prior to overflows. But water already in the bypass from other sources could partly mitigate the juvenile stranding potential, and adults that had strayed into the bypass would have a better opportunity to escape.

Summary and Conclusions:

The Tisdale Weir Project could provide substantial benefits to Sacramento River salmon. However, the proposed operation does not address potential risks on the one hand and may not fully take advantage of potential benefits on the other hand.

Figure 1. Catch of fall-run-sized salmon in screw traps in lower Sacramento River near the Tisdale Weir in winter-spring 2019

Figure 2. Proposed operation (purple shaded) of Tisdale Weir gates under dry year 2018 and wet year 2019 water level conditions. Gates could be operated at flows above the green line. The weir would normally overflow at water levels in the Sacramento River above approximately 44-ft elevation.

Figure 3. Pre-smolt catch of winter-run-sized salmon in screw traps in lower Sacramento River near the Tisdale Weir in winter-spring 2019.