Category Archives: Chinook Salmon

Sacramento River Salmon Redd Dewatering in Fall 2020

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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.

 

Butte Creek Spring Run Salmon – Status End-of-Year 2020

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When I last reported in May 2017 on the status of Butte Creek spring-run Chinook salmon, the population had hit lows as a consequence of the 2013-2015 drought.  I am happy to report the run’s rebound after the drought with new reported and revised CDFW escapement estimates.

Following escapement in 2017 that was the lowest since 1998, the population estimate increased to 6253 in 2019 (Figure 1).  The spawner-recruit relationship (Figure 2) continues to indicate a positive spawner-recruit relationship, with and positive responses to normal water year 2016 in the 2018 run and to wet water year 2017 in the 2019 run.  Though 2018 was a below-normal water year like 2016, the run in 2020 produced by 2018 water conditions has been characterized as small.1 A small 2020 run may be the consequence of the low number of 2017 spawners.  In addition, the devastating 2018 Camp fire in the watershed may have adversely affected the 2020 adult returns and future spawning runs.  But overall, the outlook for the 2021 and 2022 runs is promising given the improved number of spawners in 2018 and 2019.

Figure 1. Butte Creek spring-run salmon escapement estimates, 1975-2019.

Figure 2. Spawner-recruit relationship of spring-run Chinook salmon for Butte Creek. Numbers shown represent recruits (number of returning adults) for year displayed. The color of the number shows the conditions two years previously, when young reared in Butte Creek and then emigrated to the ocean. A red number shows a dry year rearing and emigrating conditions. Blue designates wet year rearing and emigrating conditions. Green designates normal year rearing and emigrating conditions. For example, 17 represents escapement in 2017, while its red color designates drought conditions in 2015.

Tuolumne River Salmon Runs in Decline – End-of-Year 2020 Status

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After decades of dominating the overall salmon run in the San Joaquin River watershed, the salmon run in the Tuolumne River now lags behind the runs in her sister rivers.  The Tuolumne River is a San Joaquin River tributary with no hatchery.  Its salmon runs are declining (Figure 1).  Unlike her sister rivers the Stanislaus and the Merced, the Tuolumne salmon run did not rebound as well after the 1987-1992, 2007-2009, and 2013-2015 droughts (Figure 2).

The Tuolumne run has had difficulty recovering from droughts because spawner numbers in subsequent years are too low.  There is a positive spawner-recruit relationship, heavily influenced by water year conditions (Figure 3).  Recruitment (run size) is influenced by the number of parent spawners (three years earlier), poor rearing year conditions (two years earlier), and poor conditions in the year adults return.. Runs from 1990-1992 had all three of these adverse conditions, which led to a 99% loss of their potential (two log levels).  The third years of the two recent droughts (2009 and 2015) had similar reduced potential, though with only two of the adverse conditions (poor rearing conditions and poor adult returns).

In a recent post, I related near-record-low salmon runs over the past several years in the Yuba River, a Sacramento River tributary that is similar to the Tuolumne in that it has no hatchery.  Like the Yuba, the Tuolumne salmon run is also markedly influenced by hatchery strays from other Central Valley rivers.  Hatchery strays from other rivers (Figure 4) dominate otherwise poor runs in the Tuolumne River in the years following droughts.  Many Battle Creek and Mokelumne River hatchery smolts trucked to the Bay in 2014-15 later strayed to the Tuolumne River to spawn.

Lack of returning wild salmon that are of Tuolumne River origin, and the dominance of hatchery strays after droughts, do not bode well for the native Tuolumne salmon run.  Resource agencies and other science experts have recommended maintaining a run of at least 500 native spawners for the run to remain “viable” (McClain 2010).  While recent runs since the 2013-15 drought have averaged near 1000 spawners, the fact that 60-70% are hatchery strays indicates that this goal has not been met over the past 15 years.  To increase wild salmon production, the State Water Board needs to adjust the allocation of Tuolumne River water, a process the State Water Board began in 2018.  Changes in the operation of the Delta pumps to reduce pumping during the emigration season would improve the success of all San Joaquin watershed salmon runs.  As native populations improve, river managers could reduce the influence of hatchery strays by ‘sorting out’ strays at the adult counting weir in the lower Tuolumne River; however, this would necessitate marking all Central Valley hatchery smolts.

Figure 1. Fall run Chinook escapement to the Tuolumne River 1975-2019. Data Source.

Figure 2. Fall-Run Chinook salmon escapement in San Joaquin River tributaries 1975-2019. Data Source.

Figure 3. Spawner-recruit relationship for Tuolumne River fall-run Chinook salmon. Numbers are log transformed minus 1 (2.00 = 1000). Numbers are recruits in their spawning return year. Red number is dry water year two years earlier when rearing as young. Red circle is dry year adult return year. Blue is wet year. Green is normal water year.

Figure 4. Source of hatchery strays in Tuolumne River spawning ground surveys in 2016 and 2017. Note only 25% of hatchery smolts are marked. Source.

Winter Pulsed Flow for Salmon Needed Now!

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Winter pulse flows benefit fall-run salmon fry by helping them emigrate to the Delta and Bay nursery areas (see discussion in February 2019 post). The tailwater spawning reaches of dams need reservoir releases to stimulate emigration of fry (Figure 1). Such releases piggy-back on stormwater flows in downstream tributaries, such as those in late January 2021 (Figure 2).

Nearly all Central Valley reservoirs are capturing recent high precipitation from their upper watersheds. With forecasts of further substantial rainfall into mid-February 2021, modest reservoir releases would provide substantial potential benefits to Central Valley salmon populations.

Figure 1. Sacramento River fall-run salmon fry catch near Red Bluff (river-mile 240) in winter 2020. Note that flow pulses stimulated winter fry emigration.

Figure 2. Flows from Shasta/Keswick reservoirs (river-mile 300, brown) and at downstream sites Bend Bridge (river-mile 250, green) and Wilkins Slough (river-mile 125, blue) in winter 2021. Note that tributary inflows created flow pulses in lower reaches of the Sacramento River.

Scott River Chinook Salmon Update

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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.