Category Archives: Fish (general)

American Shad – It is time to manage their populations

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I have studied American shad, a popular sportfish and anadromous herring native to the East Coast, in the Hudson, Columbia, Sacramento, American, Feather, Yuba, and Stanislaus rivers. I have also fished for them for 50 years.  They are the most abundant anadromous fish in the Bay-Delta and Columbia River watersheds.  Millions run up the Sacramento and Columbia rivers every spring to spawn.  The 1-to-6-pound adults arrive in spring and spawn from late spring into summer as waters warm.  After spawning, some die, but many adults return to the ocean.   The eggs are large like those of salmon, but. unlike salmon eggs, shad eggs float and hatch as they drift downstream toward tidewater in the Delta through late spring and summer.  Young shad then rear in the tidal estuary through the summer before heading to the ocean.

Shad interact with our native fish in various ways, most of which are detrimental.  Whether they and other nonnative fish like striped bass contribute to population declines of native species like salmon, steelhead, smelt, and sturgeon is open to debate.  I believe that coupled with changes in climate and water management, the effects of nonnative fish on native species are getting worse.

A 2017 review of the ecological role of American shad in the Columbia River (Haskell 2017) provided three hypotheses regarding the Shad’s effect on Columbia River food webs:

  1. Juvenile shad are an abundant and highly energetic food that increase the growth rate of major salmon predators [e.g. Northern Pikeminnow, Walleye, Smallmouth Bass, and Channel Catfish) – viewed as negative by supporting production of salmon predators.
  2. Juvenile shad are planktivores that compete with juvenile salmon, particularly later migrating sub-yearling Chinook Salmon in the lower Columbia River – viewed as negative by reducing food for salmon thus reducing growth and survival.
  3. Large numbers of adult shad could influence nutrient balances given their capacity to convey marine-derived nutrients – another source of marine carbon input viewed as positive.

I would add four further hypotheses/issues on the role played by American shad:

  1. Adult shad migrate from the ocean into the Bay-Delta estuary in spring on their way to spawning rivers. They number in the millions, feeding on plankton including larval fish such as newly hatched Longfin and Delta smelt, and fry salmon that frequent the estuary and lower rivers.
  2. Adult shad spend late spring and most of the summer spawning in major in the mainstem rivers and their larger tributaries, during which they feed on aquatic invertebrates and juvenile salmonids. Their spawning run in the spring coincides with the rearing of juvenile fall-run salmon and steelhead.  Shad adults can be extremely abundant during the spring emergence of fry steelhead, especially in tailwaters below dams that block shad migrations.  The American, Feather, Yuba, and Mokelumne Rivers have such conditions.  Historical anecdotes of adult shad feeding on young salmonids below the Red Bluff Diversion Dam in the upper Sacramento River are available from CDFW predator survey reports.  In my own experience, I commonly use small spoons representing salmonid fry and parr size (2-3 inches long) that are readily swallowed by feeding adult shad.
  3. Adult shad may spawn through the summer in some tributary tailwaters where cold water releases (<65ºF) are prescribed for over-summering salmonids. Cold water can extend the period of shad spawning and the period in the tidal estuary when juvenile shad compete with smelt and other fishes for zooplankton prey.
  4. Juvenile American shad rear in freshwater and low-salinity tidal zones of the Bay-Delta estuary from late spring through summer (Figures 1-6), where they feed on zooplankton of the same types as Delta smelt and other native fishes.

As is the case with many native fish species, American shad populations suffer during periods of drought.  This has been especially true in the past two decades in the San Francisco Bay-Delta Estuary (Figure 7), commonly referred to as the period of the Pelagic Organism Decline.  It is an open question whether the American shad are simply experiencing the decline like the native fish, or contributing to the native declines, or both.

The likely answer is both.  All the fish suffer in drought.  All the fish do not recover completely after droughts.  All the fish populations exhibit a long-term downward population spiral.  For some, it is a spiral toward extinction.  Even in decline, some nonnatives like American shad and striped bass can have increasing effects on the natives facing extinction.  If that is the case, then we should do everything possible to at least provide habitat conditions that favor native fish over nonnative fish.  The fact is that, in many cases, nonnative fish, including shad and striped bass, are more resilient than the native fish.  That is because the physical habitat and water management increasingly are less favorable to the native species.  We need to reverse this trend.

For more recent discussion on Central Valley American shad see:

https://calwatercenter.org/american-shad-the-deltas-most-abundant-and-least-considered-anadromous-fish/

Figure 1. Wet year 2019 American shad juvenile catch-size distribution in Bay-Delta spring 20-mm Survey.

Figure 2. Wet year 2019 American shad juvenile catch-size distribution in Bay-Delta Summer Townet Survey.

Figure 2. Wet year 2019 American shad juvenile catch-size distribution in Bay-Delta Summer Townet Survey.

Figure 3. Wet year 2019 salvage and export rates of juvenile American shad at south Delta export facilities.

Figure 4. Wet year 2019 catch distribution of juvenile American shad in September Fall Midwater Trawl Survey.

Figure 5. Wet year 2019 American shad catch distribution versus salinity (EC) for September Fall Midwater Trawl Survey. Red line indicates shad concentrate in low-salinity zone (5-15k EC).

Figure 6. Wet year 2011 Delta smelt catch distribution versus salinity (EC) for September Fall Midwater Trawl Survey. Red line indicates smelt concentrate in low-salinity zone (5-15k EC).

Figure 7. Catch index of American shad juveniles in Fall Midwater Trawl Surveys 1967-2021. Recent drought periods noted.

Yuba River Salmon in 2022

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In a December 2020 post, I described the status of the fall-run salmon population in the Yuba River.  Hatchery salmon predominate, while natural production is minimal.  The population remains in a very poor state – at about 10% of recent historical levels during and subsequent to multiyear droughts such as 2007-2009 and 2013-2015 (Figure 1).

In a January 11, 2022 post, the South Yuba River Citizens League (SYRCL) promotes cleaning the two fish ladders at Daguerre Dam half way up the river to the impassable Englebright Dam, in order to provide better passage for spawning salmon to prime spawning habitat.  Without effective ladders, salmon are delayed or even forced to spawn downstream of Daguerre Dam in marginal habitat.  The ladders must be maintained per the federal NMFS biological opinion and take permit to operate Daguerre Dam as a water diversion dam for the Yuba County Water Agency (YCWA).

SYRCL’s plea to clean the fish ladders is helpful in bringing attention to the problems facing salmon (and steelhead) in the lower Yuba River.  However, the fish ladders at Daguerre are only a small part of the problem for Yuba River salmon.  River flows and habitat in the lower Yuba River need improvement.

River Flows

It is instructive to compare flows in 2020 (Figure 2) to flows in 2021 (Figure 3), particularly at the Marysville gage, where water has passed downstream of all the local agricultural diversions at Daguerre Dam.

2020

From May through mid-August of 2020, flows at Marysville averaged about 1000 cfs (Figure 2).  The vast majority of this water was released through YCWA’s New Colgate Powerhouse upstream of Englebright Dam.  In the fiscal year from July 1, 2020 to June 30, 2021, YCWA had revenues from power sales of over $80 million. 1 Water released during the summer creates more power revenue than flows released in spring.

Better management for fish would release more of the water in the spring, providing more areas in the lower Yuba River for juvenile salmon and steelhead to grow and higher flows to move them downstream when they are ready to leave the system.  SYRCL, CSPA, and other conservation organizations, as well as staff from fisheries agencies, have recommended such a change in release pattern during the ongoing relicensing of YCWA’s hydropower project.

Some of this water released in the summer of 2020 was also sold out of the watershed, generally to entities south of the Delta.  In the fiscal year ending June 30, 2021, YCWA also made $12 million on water sales.2 The large flow increase at the end of August 2020 – likely a water sale – had no benefit for fish.  Its biggest effect on fish was that It drew down storage in New Bullards Bar Reservoir, which created a cascading effect in the very dry year 2021, when flows for all purposes were limited by lack of stored water.

2021

In a very dry year like 2021 that follows a dry year like 2020, river flows in spring and summer (Figure 3) become a major limiting factor.  First, there are no late-winter, early-spring flow pulses to attract adult spring-run salmon.  At a flow of 400 cfs at the bottom end of the lower Yuba River, there is insufficient flow to help adult spring-run salmon move upstream through many shallow riffles and through the Daguerre ladders.  Very low late-summer and fall low flows likewise hinder fall-run salmon.  Second, flows in late winter and early spring are too low to efficiently carry juvenile salmon downstream while avoiding the many predators on their way to the Bay and ocean.  Downstream of Daguerre Dam, over-summering juvenile salmon and steelhead must contend with low flows and associated stressful water temperatures.  Additionally, spawning at 400 cfs flow leads to redd scour if fall rainstorms occur: a late-October storm in 2021 brought Yuba flows up to 15,000 cfs and raised water levels nearly 10 feet (Figure 4).

Habitat

Feeding and cover habitat in the lower Yuba River are virtually nonexistent.  Predatory fish abound below Daguerre Dam.  Floodplain off-channel habitat and woody debris are severely lacking, especially during when winter-spring river flows are relatively low.  Many fall-run salmon spawn in poor spawning habitat below Daguerre.  To its credit, YCWA has contributed on a voluntary basis to several habitat improvement projects in the lower Yuba River, including the ongoing restoration at Hallwood.  However, it has vigorously resisted the establishment of regulatory requirements for additional projects.

Biological Opinion (BO)

Keeping the ladders clean is already a mandate.

  • Measures shall be taken by the Corps to minimize the effects of debris maintenance and removal at the Daguerre Point Dam fish ladders.
  • When Yuba River flows exceed 4,200 cfs, the Corps shall provide notifications to NMFS on the status of debris accumulations and fish passage conditions at the Daguerre Point Dam fish ladders.
  • The Corps shall take action within 24 hours, or as soon as it is safe, to remediate fish passage conditions related to debris maintenance and removal at the Daguerre Point Dam fish ladders.
  • The Corps shall, by January 31 of each year, report to NMFS an update on previous year’s debris maintenance and removal actions, including details on amount of debris removed, the timing of removal and the conditions that triggered debris accumulation.
  • The Corps should consider predator removal at Daguerre Point Dam.

 Summary and Conclusions

Flow regimes and habitat improvements are necessary to save Yuba salmon, in addition to ladder repairs and cleaning at Daguerre Dam.  The Yuba River Accord, which has defined lower Yuba River flows since 2008, leaves too much flow in the summer by shorting flows that salmon and steelhead need in the spring.  The channel of the lower Yuba River also needs extensive physical improvement.

Figure 1. Yuba River salmon escapement 1953-2020.

Figure 2: Yuba River flow (cfs) March 1 – September 15, 2020 above (orange) and below (blue)
Daguerre Dam.

Figure 3. Yuba River flow (cfs) March 15 – September 15, 2021 above (orange) and below (blue) Daguerre Dam.

Figure 4. River flow (cfs) and stage (feet) in lower Yuba River below Daguerre Dam near Marysville in fall 2021.

  1. See YCWA financial report for 2021 and 2020 at https://www.yubawater.org/Archive.aspx?ADID=310, pdf p. 14. ↩
  2. Id. Compare wet year 2019, with likely no out of basin water sales, and water sale revenues of $531 thousand. ↩

Delta Pumps Throttled Back – December 2021

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A January 1 article in the Bee noted federal and state Delta pumping plants were “throttled back” in late December to protect the nearly extinct Delta smelt and other fish.  Exports had reached 9000 cfs from December 17-19, 2021, and then cut to 2000 cfs on December 20, despite high Delta inflows from the Sacramento River (Figure 1).  With the Delta Cross Channel closed in December and the False River Barrier in place, exports were drawing from the interior Delta via the Old and Middle River channels (Figure 2).  Most of that water was replaced via Georgianna Slough from the Sacramento River (7000 cfs) and San Joaquin River (1000 cfs).  The overall pattern from December 19 is shown in the map below.

Map of daily average flow conditions in the Delta, December 19, 2021.

Export cutbacks in December were prompted by the federal ESA biological opinions to protect Delta smelt, as well as winter-run and spring-run salmon from the Sacramento River.  Adult smelt move up into the interior Delta from the Bay with the first late-fall, early-winter runoff events.  Juvenile salmon move downstream to the Delta during these same early storm events and move into the interior Delta via Georgianna Slough.

Historically, exports were maxed-out near 11,000 cfs during December storm flows to refill San Luis Reservoir in the San Joaquin Valley after the irrigation season.  But such high exports resulted in heavy losses of smelt and salmon at the south Delta pumping plants (Figures 3 and 4), prompting the mandates in the biological opinions for export reductions.

San Luis Reservoir at the end of December 2021 was only at 30% of its 2 million acre-feet capacity; when the historical average for December has been 60%.  There is strong pressure to refill the reservoir.  On the other hand, the smelt and salmon are endangered species on the verge of extinction after several multi-year droughts in the past 15 years.  The smelt and salmon are in the Delta now, and need protection, whereas San Luis still has a chance of filling this winter under the allowed exports if 2022 continues normal or wet.  Because Federal and state laws mandate protecting the endangered fish and the biological opinions specify priority be given to the fish under these specific circumstances, export restrictions are the appropriate prescription.

Figure 1. Delta inflow from the Sacramento River at Freeport (FPT) and San Joaquin River at Mossdale (MSD) November-December 2021.

Figure 2. Internal Delta tidally-filtered flows in Old and Middle River en route to south Delta export pumps in December 2021.

Figure 3. Exports and salvage of winter-run salmon at export pumps from December 1, 2002 to February 1, 2003.

Figure 4. Exports and salvage of Delta smelt at export pumps from December 1, 2002 to February 1, 2003.

Fall Shasta Reservoir Pulse Flow Release – needed for winter run salmon in 2021

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Flow pulses released from Shasta Reservoir are badly needed in fall to match up with downstream tributary flow events.  Such flow pulses are needed to support the emigration of young winter-run salmon from the spawning reach near Redding.  The Redding reach receives no flow pulses because fall-precipitation inflows to Shasta are retained as storage in the reservoir, even in wet years.  In a December 2018 post, I described the lack of these badly needed and widely recommended fall flow pulses.

The problem occurred in fall 2021.  Because water year 2021 was a critically dry year with near record low end-of-September Shasta storage, there was understandably a common interest in retaining inflows to the reservoir.  But since water year 2022 began on October 1, there were major Valley-wide storm events, including significant inputs into Shasta Reservoir (Figure 1).

Despite these inflows, there were only reduced releases from Shasta this fall as irrigation demands and water transfers ebbed (Figure 2).  When the flow rates in the Redding reach dropped, water levels also fell 3 to 4 feet, reducing available rearing habitat as well as flows that might stimulate emigration.  The minimal Shasta-Keswick flow releases were high in turbidity (Figure 4), due to the storm-caused erosion in the severely storage-depleted reservoir.  The stage drop and higher turbidity also hurt the fall-run spawners during the peak of their fall spawning in the river near Redding.  None of Mother Nature’s late October flow gift to Shasta Reservoir was shared with beneficial uses immediately downstream.

Further downstream, the Sacramento River received its own gifts (Figure 4), but only from downstream (20-60 miles) tributary inputs.  The young winter-run salmon in the Redding spawning reach should have been given a boost to get them to where they could have benefitted from tributary inputs to the main lower river.  Higher flows in the mainstem provide quicker and safer trips to the Delta, Bay, and ocean.

It is apparent that many of the young salmon left the spawning reach earlier, during the higher September-October flows (Figure 5).  Many of these fish spent the early fall rearing in the upper 60 miles of river in less-than-optimal water temperatures, greater than 58ºF (Figure 6).  This is another reason a flow pulse to stimulate the emigration of those juvenile salmon that remained in the uppermost and coolest reach near Redding was important.

The reason that flow rate is important is that it speeds young salmon emigration.  How fast they move to the Bay-Delta greatly influences their survival (Figure 7).  In low-flow drought years like water year 2014, the fall emigration takes longer (Figure 8). Tag data also indicate flows near 10,000 cfs improve survival over lower fall flows (Figure 9).

So what should the prescription for the fall of 2021 have been?  First, Shasta Reservoir should not have been drawn down so far as to provide release of only warm muddy water.  Second, a pulse flow of at least 7000 cfs was needed coincident with the first lower river flow-pulse event with the reservoir release sometime between October 23 and November 1.  This would have added 2000 cfs to the already existing 5000 cfs reservoir releases (see Figure 2), and 2000 cfs to the already existing 8000 cfs Red Bluff flow (see Bend flow in Figure 4).  Third, a second flow pulse of about 5000 cfs Keswick release was needed on or about December 13 coincident with the second precipitation event and Red Bluff pulse.  This would have added 2000 cfs to the already existing 3000 cfs reservoir release.  Such one-day pulse releases should be short enough in duration to make them unlikely to stimulate substantial spawning of fall-run salmon in areas where the eggs would be subject to stranding.

In conclusion, the two days with an added release of 2000 cfs to create two separate pulse flows would have amounted to 8000 acre-feet of Shasta or Whiskeytown/Keswick storage.  Whiskeytown held 200,000 acre-feet of storage of cooler, lower turbidity Lewiston Reservoir/Trinity River water that could have provided the 8000 acre-feet needed for the Keswick flow pulses.  These two flow pulses would have provided significant benefit in improving the survival of emigrating young winter-run salmon in the Sacramento River near Redding.  A December pulse would also have created benefits for the fall-run spawn.

A one-day flow pulse with an added release from Keswick of 2000 cfs in early January would still provide benefits for outmigrating fall-run salmon.

Figure 1. Four significant precipitation events produced 5000 to 13,000 cfs daily inflow to Shasta Reservoir in fall 2021.

Figure 2. Flow and stage in the Sacramento River below Keswick Dam near Redding in fall 2021.

Figure 3. Water temperature and turbidity in the Sacramento River below Keswick Dam (KWK, RM 300) and above mouth of Clear Creek (CCR, RM 290) near Redding in fall 2021. Red line is 7 NTU turbidity above which eggs and embryo salmon in spawning redds are adversely affected.

Figure 4. Daily flow average (cfs) of Sacramento River below Keswick Dam (KWK, RM 300), at Bend Bridge (BND, RM 240), and at Wilkins Slough (WLK, RM 140) in fall 2021.

Figure 5. Passage rate of juvenile winter run salmon at Red Bluff screw traps and nearby Bend Bridge gage flow summer-fall 2021. Note increased catch rate during pulse flow events.

Figure 6. Water temperature (F) in the Sacramento River below Keswick Dam (KWK, RM 300) and at Red Bluff (RDB, RM 240) in fall 2021.

Figure 7. Estimated survival rate from Redding to Delta for juvenile salmon per the number of days spent upstream. Source: NMFS presentation.

Figure 8. Cumulative passage of winter-run at Red Bluff screw traps 2007-2013. Note longer period of passage in fall 2013 for Brood Year 2013. Source: USFWS Red Bluff.

Figure 9. Survival of juvenile salmon (acoustic-tagged wild and hatchery spring-run and fall-run salmon) as a function of flow in upper Sacramento River from Red Bluff (RM 240) to the Delta (RM 100). NMFS, Santa Cruz: “Nonlinear survival of imperiled fish informs managed flows in a highly modified river”. Cyril J. Michel $, Jeremy J. Notch, Flora Cordoleani, Arnold J. Ammann, Eric M. Danne. First published: 19 May 2021 doi.org/10.1002/ecs2.3498. Ecosphere / Volume 12, Issue 5 / e03498

Fall-Run Salmon Spawning near Redding 2021 A tough year for the fall-run salmon spawn

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Fall-run salmon spawn in the fall in the 20-40 miles of the Sacramento River downstream of Keswick Dam near Redding. Numbers of in-river fall-run spawners have declined severely over the past several decades (Figure 1). Declines were worst three years after drought periods (2007-2009, 2013-2015), due to poor egg and fry survival during droughts. A February 2021 post discussed the role of redd dewatering and fry stranding from severe drops in flow and water level (stage) as major drought-related factors in the escapement declines. A 2018 post listed a broader range of factors, including high water temperatures during droughts in addition to stranding.

Stranding was once again a major factor in fall 2021 as water levels near Redding dropped 4 feet from October to November (Figure 2). Further downstream in the lower spawning reach, salmon have also had to contend with high flows as well (Figure 3). High flows (1) encourage salmon to spawn in margin habitat that later dewater, and (2) cause scouring of redds spawned earlier at lower water levels.

In fall of drought year 2021, an additional severe-mortality factor has become apparent. Turbidity/suspended sediment levels in the spawning reach (Figure 4) were at or above lethal levels for salmon eggs and embryo (see December 23, 2021 post) for most of November, a peak spawning period. The late-October record storm and subsequent further rain and runoff have elevated inflows to Shasta Reservoir. As these higher flows have entered the reservoir, they have eroded vast areas of sediment exposed in the drought-depleted reservoir.1 The suspended sediment has carried through the reservoir into the spawning reach below Keswick Dam.

Of positive note, the higher flows (Figure 3) and associated turbidity have likely helped salmon fry that spawned earlier in tributaries like Battle Creek and Clear Creek move downstream in the Sacramento River toward the Delta and Bay.

In summary, fall-run salmon spawning in the most upstream reach of the lower Sacramento River near Redding have faced extreme habitat conditions in 2021. These conditions began with high October water temperatures from a depleted cold-water-pool in Shasta Reservoir. Next came a four-foot drop in water level due to sharply reduced Shasta Reservoir releases. Added to these traumas were egg-smothering levels of suspended sediments from Shasta Reservoir caused by erosion of drought-exposed, decades-old reservoir sediment during a record-level late October storm and subsequent runoff events.

Figure 1. In-river fall-run Chinook adult escapement to the upper Sacramento River 1952-2020.

Figure 2. Streamflow (cfs) and water surface elevation (stage) in the Sacramento River immediately below Keswick Dam October 1 – December 15, 2021.

Figure 3. Streamflow (cfs) and water surface elevation (stage) 50 miles below Keswick Dam October 1 – December 15, 2021. High flows were from tributary inflows below Redding (Cow Creek, Battle Creek, Clear Creek, and others).

Figure 4. Water temperatures and turbidities below Keswick Dam (RM 300) and above the mouth of Clear Creek (RM 290) October 1 – December 15, 2021. Red line depicts literature-based, severe-mortality turbidity level for eggs and embryo salmon for a one-day exposure.

Figure 5. Spring and fall run salmon fry catch at Red Bluff (RM 240) screw traps August – November, 2021. Also shown are nearby Bend Bridge water temperature and flow, and Red Bluff turbidity.