Author Archives: Tom Cannon

NEW FEDERAL BIOLOGICAL OPINIONS IN ACTION

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New federal biological opinions (BO’s) for the long-term operation of the Central Valley Project and the State Water Project in the Delta have been “protecting” salmon and smelt for several months. The record in practice is not good.

The ostensible purpose of the new BO’s is to protect native fishes, including ESA-listed salmon and smelt. A key focus in the new BO’s (as in prior BO’s) is on regulating reverse flows in Old and Middle River channels of the central Delta (Figure 1). Reverse or negative net upstream flows are caused by south Delta federal and state exports. Rules limiting negative OMR flows limit south Delta exports.

The U.S. Fish and Wildlife Service summarizes OMR operation, in part, as follows:1

Old and Middle River Flows

The new BO’s make a commitment to stay within the Delta pumping-related loss experienced under the 2008-09 BO RPA’s. Old and Middle River Reverse flows are to be limited based on timing (no greater than -5,000 cfs Jan-Jun); water quality conditions (short term protections for first flush events); storm event flexibility (can increase beyond -5,000 cfs if there is not a risk to the species); observed annual salvage and loss (specific triggers for loss values similar to those seen under the 2009 RPA); cumulative loss and outcomes from independent review panels.

 

Controlled OMR Flows

The action is consistent with Action 1 of the 2008 RPA by providing for integrated early winter pulse protection which requires reducing exports for 14 consecutive days so that the 14-day averaged OMR index for the period shall not be more negative than -2,000 cfs, in response to “First Flush” conditions in the Delta. In addition, once OMR management begins, Reclamation and DWR will operate to an OMR index no more negative than a 14-day moving average of -5000 cfs, unless a storm event occurs, until that point in which OMR management ends in a season (when temperatures in south Delta become lethal or June 30, whichever is earlier). The Integrated Early Winter Pulse Protection action may occur more frequently than Action 1 in the 2008 RPA, providing equal or greater protection.

To evaluate whether the new BO’s met these new commitments in December 2019 and January 2020, the reader should review Figures 2, 3, and 4 below, and also https://www.usbr.gov/mp/cvo/vungvari/OMR_Jan2020.pdf.

My own review indicates that what looked like, walked like, and quacked like a “first flush” occurred in mid-December. The lack of OMR limit protections and the allowance of maximum exports during and after the first flow pulse under the new BO’s in December 2019 led to what appear to have been grave risks to endangered salmon and smelt.2 The highly negative OMR flows in December were highly unusual and were not the norm under the prior BO’s (Figures 5 and 6). Regardless of the purported commitment to protect Delta native fishes in the new BO’s, Figure 4 shows the real effect of the new BO’s: the export of more water to southern California.

Figure 1. Old and Middle River and direction of negative net OMR flows.

Figure 2. Net daily-average OMR flows in the south Delta 11/11/19-1/17/20. Note the extremely negative flows during December that occurred because high south Delta exports are permitted under the new BO’s. Flow remained highly negative even during the period of higher outflow in early December shown in Figure 3. Source: CDEC.

Figure 3. Net Delta outflow 11/11/19-1/17/20. Note pulse of outflow from spate of storms in first half of December. Source: CDEC.

Figure 4. Export rates (cfs) at the federal Tracy (TRP) and state Harvey Banks (HRP) pumping plants in November-December 2019. Rates were near maximum throughout December.

Figure 5. Middle River flow 11/15/2019-1/20/2020 with average for prior 21 years.

Figure 6. Old River flow 11/15/2019-1/20/2020 with average for prior 22 years.

  1. Biological Opinions for the Reinitiation of Consultation on the Long Term Coordinated Operations of the Central Valley Project and State Water Project – Summary (USFWS 10/1/2019).  https://www.fws.gov/sfbaydelta/cvp-swp/documents/ROC_on_LTO_Summary_FINAL.pdf ↩
  2. http://calsport.org/fisheriesblog/?p=2981, http://calsport.org/fisheriesblog/?p=2991, http://calsport.org/fisheriesblog/?p=3006 ↩

Hatchery Steelhead Smolts Released Just in time to Chow Down on Baby Salmon

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The state and federal hatcheries in the Central Valley will be releasing 1.5 million yearling steelhead smolts this winter. The location and timing of these releases could not be worse for the survival of newly emerged wild fall-run and spring-run salmon.

The U.S. Fish and Wildlife Service released approximately 600,000 smolts from the Coleman Hatchery on Battle Creek into the Sacramento River near Redding in January. The California Department of Fish and Wildlife will release approximately 900,000 steelhead smolts from state hatcheries to the lower American, Feather, and Mokelumne Rivers in February. The peak of newly emerged salmon fry is January in the Sacramento River near Redding and February in the three tributary rivers (the difference is a result of managed fall water temperatures).

In prior posts,1 I warned of releasing yearling hatchery smolts on top of wild salmon fry (see photo below). The solution is to simply stop doing this. The fish agencies should release the mitigation hatchery smolts earlier or later in the year, or truck them to the Delta or Bay as they did in the past. In general, the agencies should also release steelhead smolts during high flows, when juvenile salmon have a greater chance to evade the steelhead, and when both steelhead and salmon are likely to move more quickly downstream.

In the longer term, the California Department of Fish and Wildlife and the U.S. Fish and Wildlife Service should redirect their steelhead hatchery programs toward recovery of the native steelhead stocks by converting their efforts to conservation hatchery programs. Many of the native steelhead traits are less intrusive on the salmon (e. g., fall and spring migrations, spring spawning). The fish agencies should also stop using stocks whose origin is out-of-basin (American River).

Photo: yearling hatchery steelhead smolt fed on wild salmon fry in American River in February. (Photo by author)

 

 

 

Stanislaus River Salmon in 2020

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The San Joaquin River watershed has contributed up to a third of the total Central Valley salmon run as recently as 2017, if one counts the Mokelumne River as a San Joaquin River tributary and includes its large hatchery contribution. Though the fall salmon run in the Stanislaus River includes many hatchery strays from throughout the Central Valley, the Stanislaus remains the biggest contributor of wild-produced salmon in the San Joaquin basin (Figure 1).

The Stanislaus spawner-recruit relationship (Figure 2) derived from escapement estimates indicates a positive relationship influenced by water-year type. Wetter years (blue) on average provide 10 times the recruitment per spawner as drier years, with normal years providing intermediate recruitment. Severe droughts in the 60’s, 70’s, 80’s, 90’s, and 00’s depressed recruitment and led to declining population trends. Recruitment during 2014-2018 drought-influenced period was much higher than in the prior droughts, thus maintaining a higher recent average population level. In a December 2019 post, I attributed the improvement to increases in hatchery strays as well as to spring and fall pulsed flows from prescribed reservoir releases (Figure 3). The spring flow pulses benefit smolt emigration survival. Fall flow pulses provide attraction flows as well as better spawning conditions (flows and water temperature).

Separating all the factors influencing recruitment is a challenge, but it is critical to prescribing future management. In a recent paper, Sturrock et al. 2019 found that emigrants-per-spawner and recruits-per-spawner through 2014 strongly related to within‐season stream flow variability during the winter-spring juvenile rearing period.

Variability in flow comes from storms, prescribed flow releases, and flood releases.1 Strong runs in drought-influenced 2015 and 2016 were likely higher due to the significant prescribed spring flow pulses in 2013 and 2014 (Figure 3). The strong run in 2017, despite overall poor drought-year 2015 flows (Figure 3), is likely related to the attraction of stray wild and hatchery spawners to late summer and fall prescribed pulsed flows and associated cool waters of the Stanislaus River in 2017 (Figure 4). Most of the 2015 Central Valley hatchery smolt production was trucked to the Bay and subject to high straying rates. The lower San Joaquin and Stanislaus rivers provided good attraction flows and cooler waters in 2017 to accommodate adult Central Valley salmon less inclined to seek their natal streams in routes warmer than the San Joaquin and Stanislaus rivers.

Based on studies of salmon in the Stanislaus, Sturrock et al. (2019) provide recommendations to improve recruitment per spawner and diversity of the life-history portfolio. In recent years, recruitment in the Stanislaus has been overly dependent on the success of parr and smolts emigrating in the early spring. Survival of emigrating fry in winter and older smolts in late spring has been poor. Analyses of otolith cross-sections (ear bones) of returning adults indicated a dominance of the early spring parr-smolt life-history pattern. Quotes below in italics are from Sturrock et al.

  1. Fry emigration success has suffered from reduced winter flow peaks (In years lacking winter pulse flows, salmon tended to emigrate later, larger, and in lower numbers… predicted fry expression was 62% lower following major dam construction… Even marginal improvements to fry survival rates could significantly boost adult recruitment rates.” Winter flow pulses would increase the contribution of fry emigrants to recruitment.


  2. Parr and smolt emigration success benefitted from CVPIA/VAMP Apr-May prescribed storage releases and reduced south Delta exports. “Peak parr emigration in April coincided with managed releases intended to improve downstream survival.” Continue these early spring prescriptions.


  3. Late spring smolt emigration survival has been very low due warm water temperatures and low flows. Late spring pulse flow prescriptions would increase the contribution of older smolt emigrants to recruitment.


  4. “[S]trong suppression of any life‐history diversity—whether evolved or plastic— could have serious demographic and evolutionary consequences… negative population growth in the absence of demographic rescue by hatchery strays.” Without flow pulses in winter, early spring and late spring, the population is at risk of significant decline and loss of genetic integrity. Hatchery strays will further dominate the population and production of wild fish will decline.

Other measures suggested by Sturrock et al. (2019) included:

  • Increasing fry floodplain habitat downstream of the Stanislaus to increase fry emigrant success and the contribution of the fry emigration component of the life history portfolio to adult recruitment. “Given the substantial numbers of fry often produced, even marginal increases in their survival rates would have significant impacts on recruitment.”


  • Increasing the portfolio diversity for other Central Valley salmon populations will reduce the overall risks to Central Valley fall run salmon because “[a]djacent watersheds often experience similar climates and manage their dams for similar goals, which could homogenize emigration timings among nearby populations. Shared bottlenecks such as the Sacramento‐San Joaquin Delta could further compress emigration timings, increasing the risk of match‐mismatch events in the ocean.”

In conclusion, the Stanislaus River fall-run salmon population dynamics provide important lessons for sustaining wild salmon in the Central Valley. Sustaining life history diversity will increase salmon recruitment per spawner. It will also reduce risks of population declines and loss of genetic integrity in the wild component of salmon populations.

Figure 1. Stanislaus River fall-run Chinook salmon run (adult escapement) estimates 1952-2018. Note completion date for New Melones Dam in red. Data source: CDFW.

Figure 2. Spawner-Recruit relationship for fall-run Chinook for the Stanislaus River. Number represents recruit year (escapement for that year). Color represents water year type for San Joaquin basin during brood year rearing (two years prior). Blue is wet year. Red is dry-critical year. Green is normal year. Red circle is for poor ocean rearing conditions and/or poor river flows during spawning run. For example: year 08 represents 2008 recruitment (escapement) from 2005 spawners (both log10 -1 transformed); blue represents wet year 2006 during river rearing; red circle represents poor ocean rearing and poor river flows during 08 spawning run.

Figure 3. Stream flow in the lower Stanislaus River near Ripon in 2007-09 and 2013-15 drought years. Note prescribed reservoir releases in April-May 2013 and 2014 and October of most years.

Figure 4. Stream flow and water temperature in the lower Stanislaus River at Ripon and Orange Blossom Bridge in wet year 2017. Note water temperatures below 60oF are optimal for fall spawning. The strong spring flow pulse should lead to good 2019 adult recruitment.

  1. Flood releases are rare in the Stanislaus watershed, where storage capacity is twice annual average runoff. ↩

Predators versus River Flow

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I keep emphasizing the need for fall flows to get Central Valley salmon fry, fingerling, sub-yearling smolts, and yearling smolts to and through the Delta to the Bay. This especially applies to wild spring-run and to wild and hatchery winter-run and late-fall run, the Chinook salmon runs most in danger of extinction. Extinction comes from population decline and loss of genetic diversity from lower river flows and fragmented habitat. 1

The reason river flow is important is that flow affects habitat, growth, migration, and predation of emigrating salmon.

The long, slow reservoirs behind the mainstem dams on the Columbia River studied by Conner and Tiffan (2012)2 have habitat similar to the long, slow reaches of the lower Sacramento and San Joaquin rivers in the Central Valley. Furthermore, the Delta with its tides acts as a “main-stem” dam, slowing the outward movement of water through the Delta and salmon exiting to San Francisco Bay. The Delta has also been described as the place “where predators meet prey” – where the effectiveness of predation and the role played by “Anthropogenic Contact Points” is accentuated by modified freshwater flows.

The Sacramento River channel at Walnut Grove is one of the key “anthropogenic” contact points in the Delta. The major outlets from the Sacramento River channel to the central Delta, the Delta Cross Channel and Georgiana Slough, are located here (Figure 1). Lehman et al. (2019)3 describe the predator contact points at this location in Figure 1, including submerged aquatic vegetation, rip-rapped levees, docks, and diversions. The role of these particular contact points in predation on juvenile salmon is no doubt significant.

Lehman et al. point out the difficulty in removing the predators and the problematic contact infrastructure. However, they don’t address the role river flow and associated hydrodynamics play in modifying the effects of predators or specific contact points.

In the fall during the peak of winter-run emigration, Walnut Grove is the place where the Sacramento River channel in the north Delta slows and is “diverted” into the abyss of the central Delta. Few salmon escape the central Delta’s many predators and its “anthropogenic contact points”, including the south Delta export pumping facilities. Under low Sacramento River fall inflows (around 12,000 daily average flow at Freeport), high tides cause most of the water and salmon coming down the Sacramento River to divert into the central Delta via the Delta Cross Channel (DCC) and Georgiana Slough (Figure 2). Those young salmon remaining in the Sacramento channel are then vulnerable to the contact points and predators under lower water velocities. If river inflows are higher and the DCC is closed, the risks to young salmon is greatly reduced (Figure 3).

In conclusion, the Lehman study funded by the Metropolitan Water District describes the role of predators and contact point infrastructure including submerged aquatic vegetation, docks, riprap, and diversions. However, the Lehman study does not address the key factors in the fall loss of juvenile fish in the Delta: lower flows and the diversion of water into the central Delta for export. Closing the Delta Cross Channel and increasing river flows are the prescriptions needed to cut losses of emigrating endangered Central Valley salmon. Cutting south Delta exports in the fall would also be beneficial.

Figure 1. Predation contact points near Walnut Grove in the north Delta. Source: From Lehman et al. 2019.

Figure 2. Measured streamflows at USGS gages near Walnut Grove on 12/1/2019 at 8:00 am high tide. The DCC was open and the Sacramento River at Freeport inflow to the Delta was 12,500 cfs.

Figure 3. Measured streamflows at USGS gages near Walnut Grove on 12/5/2019 at the noon high tide. The DCC was closed and the Freeport inflow to the Delta was 21,000 cfs.

  1. Sturrock et al. 2019. https://onlinelibrary.wiley.com/doi/10.1111/gcb.14896 ↩
  2. Connor, W. P., and K. F. Tiffan. 2012. Evidence for parr growth as a factor affecting parr-smolt-survival. Transactions of the American Fisheries Society 141:1207–1218, 2012. ↩
  3. Lehman, B.M., et al. 2019. https://escholarship.org/uc/item/2dg499z4 ↩

Scott River Coho Salmon Run – Status Fall 2019

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The Scott River Coho salmon population is one of the last remaining self-sustaining wild Coho salmon runs in California and in the Southern Oregon Northern California Coho (SONCC) Evolutionarily Significant Unit (ESU).  The SONCC ESU is listed as “threatened” under the federal and California endangered species acts.  The ESU includes the Rogue River in Oregon and the Klamath River in California.

The Scott Coho run is the major wild Coho population in the Klamath River system.  Scott Coho spawn and rear in Scott Valley, once called “Beaver Valley,” located near Fort Jones.  The run has numbered over 1,000 adult Coho spawners as recently as 2013, but numbered less than 100 as recently as the 2008-09 drought years (Figure 1).

Scott Coho include three distinct sub-populations that have developed because the vast majority of spawners are three years old.  One subgroup, the 2007-2010-2013 sub-group, dominated the population in the recent past, but declined sharply in 2016.  The other two sub-groups have increased slightly since 2008 and 2009 lows.

The spawner-recruit relationship (Figure 2) shows a generally positive relationship between the number of spawners and recruits three years later for each sub-group and the overall population with one distinct outlier (the sharply lower 2016 run).  So why was the 2013 run so high and the brood-year 2013 run in 2016 so poor?

1.      2013’s Good Run

The 2013 run (brood year 2010) got off to a great start in wet water year 2011.  Flows for the fall 2010 spawning run were good from November through January [Figure 3), which ensured spawner access and good spawning conditions throughout Scott Valley.  Flows were also good through the spring and fall of 2011 (Figure 4), ensuring good smolt production and a subsequent strong run in 2013.

2.      2016’s Poor Run

The strong run in 2013 spawned in brood year 2013, which got off to a rocky start in dry water year 2013-14.  Flows in fall-winter 2013-14 encountered by the strong 2013 run were very low through the early winter spawning season (Figure 5), leading to an unusually protracted run of adult spawners (Figure 6) and poor accessibility to good spawning areas.  Spawning habitat quality and quantity likely also suffered from low flows.  Flows were then very low from spring through fall of 2014 (Figure 7), likely resulting in poor over-summer survival and low smolt production for brood year 2013.

In conclusion, the Scott Coho salmon population continues to suffer from low seasonal streamflow, especially in drought years like water year 2013-14.  The population would benefit from improved summer-through-fall streamflows.  It will also benefit from the watershed habitat restoration actions being implemented by landowners, CalTrout,  the Scott River Watershed Council, Siskiyou RCD, Scott River Water Trust, California Department of Fish and Wildlife, Quartz Valley Indian Reservation, and other stakeholders.

Figure 1. Escapement of adult Coho salmon to the Scott River from 2007 to 2019. Data source: CDFW, Yreka, CA.

Figure 1. Escapement of adult Coho salmon to the Scott River from 2007 to 2019. Data source: CDFW, Yreka, CA.

Figure 2. 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 significant outlier in 2016. The Yellow line is trend-line for years other than 2016.

Figure 3. USGS gaged daily average flow (log scale) in lower Scott River, Klamath River tributary, 9/1/2010-2/1/2011, with 78 year average daily median flow for that date.

Figure 4. USGS gaged daily average flow (log scale) in lower Scott River, Klamath River tributary, 4/1/2011-11/1/2011, with 78 year average daily median flow for that date.

Figure 5. USGS gaged daily average flow (log scale) in lower Scott River, Klamath River tributary, 9/1/2013-2/1/2014, with 78 year average daily median flow for that date.

Figure 5. USGS gaged daily average flow (log scale) in lower Scott River, Klamath River tributary, 9/1/2013-2/1/2014, with 78 year average daily median flow for that date.

Figure 6. Scott River adult salmon collection weir counts of Coho salmon for fall-winter 2013-14. Data source: CDFW Yreka, CA.

Figure 7. USGS gaged daily average flow (log scale) in lower Scott River, Klamath River tributary, 4/1/2014-10/31/2014, with 78 year average daily median flow for that date.