Category Archives: Fish (general)

Low Spring Flows Reduce Survival of Spring-Run Salmon – Lessons 14 and 15

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Following an introductory post, this is the fifth 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.  This post addresses NMFS’s Lessons #14 and #15.

NMFS acknowledges that low spring flows may lead to low survival of juvenile spring-run Chinook salmon during their emigration to the sea.  NMFS also suggests that disease may also cause poor survival in dry years.

Some additional observations regarding outmigration are appropriate.  Most wild spring-run fry, fingerling, and pre-smolts emigrate in winter, although spring smolt emigration also occurs.  Another thing to consider is that while disease may be more prevalent in spring of dry years, it may be due to extended rearing in the poor habitat of the upper river in drier years (less food, warmer water, and more stress).  Increased predation by striped bass and other predators under these same habitat conditions is almost certainly another factor.  Lower flows make predators more effective because of lower turbidities, warmer and shallower water, less cover, and slower transport rates.

NMFS’s Lessons 14 and 15 did not consider lower survival of adult salmon migrating upstream in spring of drier, low flow, warmer water years.  However, this is also important.  Run counts are strongly related to water-year types, with poor runs in drier years (Figure 1).  Adults that migrate upstream in spring and over-summer in dry years face more difficult passage in spring and warmer spring and summer water temperatures.  Warmer water temperatures lead to greater stress, energy loss, and disease, poorer pre-spawn survival, and reduced reproductive success (Richter and Kolmes 2005).

An overall lesson is that low winter-spring flows lead to higher water temperatures in the lower Sacramento River migration corridor (Figures 2 and 3) and in spawning tributaries (Figure 4), which in turn reduce survival and reproductive success of spring-run salmon.

A related issue at play relates to Lesson 8 (low flows in the lower Sacramento River at the Wilkins Slough gage).  Low spring and summer flows in the lower mainstem Sacramento River flows lead to warmer spring and summer water temperatures.  This in turn leads to higher predation rates on juvenile salmon and poorer adult survival and reproduction success.  Continuing to ignore long-ago established water quality standards for water temperature and operating norms for flow is putting greater stress on all the salmon runs and on sturgeon.  Spring-run salmon are especially vulnerable because both juveniles and adults are present in the lower Sacramento River in spring.

One especially damaging case occurred in early spring 2018.  A series of storms raised flows in the lower Sacramento River by approximately 50,000 cfs, while at the same time there was only a minimum release of about 3000 cfs into the upper Sacramento River from Shasta Dam.  Substantial flows entered the lower Sacramento River from tributaries and from the outfalls of agricultural basins, including the Butte Basin at the Butte Slough Outfall gates.  Some flow even left the river via overflow weirs into the Sutter Bypass. The sudden surge of urban and agricultural basin stormwater, with high oxygen demand, sediment, and chemical loads, led to a series of fish kills of adult spring-run salmon in the lower Sacramento River at the Butte Slough Outfall (Figures 5 and 6).  It is not clear exactly why high concentrations of stormwater may have increased mortality of spring-run salmon in 2018.  What is clear is that low Shasta releases contribute to higher concentrations of stormwater in river flows at key times during their migration.

In conclusion, Reclamation should consider higher spring releases from Shasta in drier years like 2021 to (1) improve juvenile spring-run emigration survival to the Bay-Delta, and (2) improve adult spring-run survival and reproductive success.  Reclamation should also consider spring pulse flow releases from Shasta-Keswick to emulate natural unimpaired lower river spring flows and to enhance migration success.  Such pulses should be timed with lower river tributary flow pulses.  Finally, as discussed in previous posts, Reclamation’s contractors and others must reduce dry-year water diversions in spring from the mainstem Sacramento and its tributaries to further protect spring-run salmon.

Figure 1. Relationship between Mill and Deer Creek spring run salmon counts 1963-2019. Blue dots represent above-normal and wet years. Yellow dots represent below-normal and dry years. Red dots represent critical dry years. Red margin on blue dots represents a wet and above normal year for adult immigration with a critical dry year two years prior during rearing and emigration. Of special note are the sharply higher run sizes in wet years in Deer Creek, but lower run sizes in Deer Creek in drier years. This shows that production of salmon in Deer Creek suffers proportionally more than in Mill Creek in drier years. In both creeks, salmon runs suffer in years when they are emigrating and immigrating in dry conditions.

Figure 2. River flows (1000s of cfs) in the lower Sacramento River at Wilkins Slough (below the mouths of Deer and Mill Creeks) in winter-spring from 1995-2021. Note very wet conditions in 2006 and very dry conditions in 2014 and 2015.

Figure 3. Water temperatures in the lower Sacramento River at Wilkins Slough (below the mouths of Deer and Mill Creeks) in winter-spring from 2013-2021 (only data available). Note the extraordinarily warm water (near or above 70ºF) in early spring of drier 2014, 2015, 2018, and 2020. State standard is 68ºF. Migrating adult salmon suffer stress and mortality at water temperatures above 60ºF.

Figure 4. River flow and water temperature in Deer Creek 2011-2921. Wet year spring in 2011, 2017 and 2019 shown in blue highlight: other spring conditions shown in yellow highlight. Dry years include 2013-2015 and 2021. The remainder are normal or average year types. Note lower water temperatures in wetter years, with highly stressful temperatures (>68ºF, 20ºC) delayed further into spring than during drier years.

Figure 5. Dead adult spring-run salmon floating at the mouth of Butte Slough Outfall in the Sacramento River in March 2018. Fish likely died from severe stress from low oxygen and heavy suspended sediment and chemical load after being attracted to stormwater flow from outfall gates.

Figure 6. Dead adult spring-run salmon floating at the mouth of Butte Slough Outfall in the Sacramento River in March 2018. Fish likely died from severe stress from low oxygen and heavy suspended sediment and chemical load after being attracted to stormwater flow from outfall gates.
Source: https://youtu.be/t5oB_hWcrzU

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.

Scott River Coho 2020 Run Improves

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I last updated the status of Coho salmon in the Scott River, a major Klamath River tributary in northern California east of Yreka (Figures 1 and 2), in a January 2020 post. At that time, I lamented on the decline of the strongest distinct population subgroup, 2013-2016-2019, exemplified by the weak run in 2016 caused by the 2013-2016 drought. In this post, I am happy to report on the strong 2020 run and the surprise improvement of the 2014-2017-2020 subgroup (Figure 3).

The improvement in the 2020 run, despite a sparse spawning run in late-fall 2017, is likely a consequence of good water conditions in early water year 2018 (Oct 2017-Sep 2018, Figure 4) after wet water year 2017. The run had good access to spawning habitat and early rearing conditions from fall 2017 through the spring of 2018. The young coho were sustained though the dry summer of 2018 in spring-fed reaches of the upper river and its tributaries. Spring-fed habitats likely benefitted from the abundant winter 2017 snowpack. The Scott watershed had also benefitted from significant restoration of its over-summering habitat over the past decade.1

The yearlings of brood year 2017 then had good wet year emigrating conditions in late fall 2018 and early winter 2019 (Figures 4 and 5). There were multiple winter flow pulses to help the yearling coho smolts emigrate from Scott Valley and on down the Klamath to the ocean.

In summary, the spawning run in fall 2020 (from brood year 2017) was exceptional, benefitting from conditions that were a consequence of wet years 2017 and 2019. Over-summering survival in dry year 2018 was likely good because of good spring-fed flows and habitat in the upper watershed, a carryover from the good 2017 snowpack and restoration of beaver-pond habitat by Scott Valley stakeholder groups. This one small success bodes well for recovering other salmon and steelhead populations throughout the Klamath watershed, especially in a future dominated by climate change.2

Figure 1. Klamath River watershed with the Scott River west of Yreka, CA. (Source DOI.)

Figure 2. Google Earth view of the Scott River watershed with its snow-covered Marble Mtns to the west and the Trinity Alps to the south. Scott Valley, with its green hay fields from Etna to Fort Jones, was once called “beaver valley” due to its abundance of spring-fed beaver ponds and meadow streams ideal for over-summering salmon and steelhead.

Figure 3. Spawner-recruit relationship for Scott River Coho salmon. The number represents recruits (spawner counts) for that year versus spawners counts from three years earlier. For example: “13” represents spawner counts (recruits) in fall 2013 versus spawner numbers three years earlier in 2010. Number color represents different spawner subgroups (blue=subgroup 10-13-16-19). The Red circle highlights the significant outlier in 2016. The Yellow line is trend-line for years other than 2016 and 2020. Data source: CDFW weir counts.

Figure 4. Scott River streamflow measured downstream of Fort Jones as the river leaves Scott Valley, September 2017 to April 2019. Note the near average wet winters in 2018 and 2019, and dry summer in 2018 typical of the Mediterranean climate of northern California. The drier-than-average summer 2018 is indicative of water use for hay-pasture irrigation.

Figure 5. Klamath River streamflow measured downstream of the mouth of the Scott River, October 2018 to June 2019. Note the near average wet winter-spring with five distinct flow pulses typical of wetter years. of the Mediterranean climate of northern California. The flow pulses helped yearling coho from brood year 2017 emigrate to the ocean. The adults from brood year 2017 returned in late fall of 2020.