Category Archives: Water Quality

How Protective is the State’s Plan for Delta Fishes?

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California’s Attorney General has sued the federal government over the new federal biological opinions for the operation of the Central Valley Project (CVP) and the State Water Project (SWP). But in fact, the State’s plan for operating the Central Valley operations of the State Water Project is not much better than the Bureau of Reclamation’s federal plan in terms of protecting Delta fish. The State’s plan is built on the same theory that the water projects can divert more water by monitoring fish presence and backing off on diversions when monitoring detects fish. This so-called “real-time operation” was also the foundation of the Department of Water Resources’ (DWR) proposal to protect fish in the 2016-2019 hearings on DWR’s proposed Delta tunnels (“WaterFix”).

The major difference between the new state and federal plans for Delta operations is that the State plan retains a requirement for increased flow in the summer and fall of wetter water years to protect smelt. The State’s draft EIR for the Long Term Operation of the State Water Project (LTO EIR) describes the proposed Summer-Fall X2 Action for Delta outflow (Figures 1 and 2). The action/criteria proposed is to maintain “X2” (the location in the Bay-Delta where salinity measures ~2 ppt chloride, or 3800 EC) under prescribed limits in summer and fall months by water-year type.

The LTO EIR describes two alternatives: the Proposed Project and Alternative 4.1 Both would limit monthly average or 14-day average X2 at river kilometer 80 (near the CDEC Collinsville gage). The Proposed Project includes only September and October X2 objectives, while Alternative 4 also covers June-August for wet years. Under both alternatives, criteria also include opening the Suisun Marsh Salinity Control Gates (SMSCG), an action to reduce EC at Collinsville gage and in Suisun Marsh and Montezuma Slough, which would raise salinity in eastern Suisun Bay.

I discussed the ramifications of the federal Biological Opinions in a September 2019 post. The only major beneficial change that the LTO EIR proposes is adding summer X2 criteria in Alt 4 to extend outflow protection from June 20 to August 31. The new Fall X2 requirement (September-October) in the LTO EIR would be less protective than existing Fall X2 objectives, because the new state requirement would move the compliance point upstream from km74 to km80.

In order to understand how the state’s proposed new Summer-Fall X2 requirement would work, I examine below how the action might have applied in recent water years 2016-2019, two below normal water years and two wet water years..

Below Normal Water Years 2016 and 2018

Under the LTO EIR criteria (both the Proposed Project and Alt 4 alternatives), the X2 location and low salinity zone would be similar to historical 2016 conditions (Figure 3), except that outflow could be lower and salinity higher in June, when there would be higher exports, less outflow, and a warmer more upstream low salinity zone (Figure 4). The main benefit of the X2 Action under Alt 4 would be that it would extend the D1641 agricultural salinity standards past June 20 by making them also apply from June 20 through August. Both the D1641 and Alt 4 criteria allow significant daily variation in X2: 14-day and monthly averages.

In 2018 (Figure 5) there would be a similar potential negative effect in June and a positive benefit in August under Alt 4.

Wet Water Years 2017 and 2019

Under the proposed LTO EIR criteria for wet years, Fall X2 criteria (September-October) would be the same as described above for below normal years. This would weaken protection in comparison with the previous Fall X2 requirements in the 2008-09 biological opinions (Figures 6 and 7). Summer (June-August) criteria would be generally less protective than existing D1641 salinity standards for wet years. If the State were to adopt the LTO EIR summer criteria, salinities would be higher and the low salinity zone further upstream and warmer than occurred in June-August of wet years 2017 and 2019. This would allow higher exports.

Summary and Conclusion

Under both the Proposed Project and Alternative 4, the LTO EIR’s Summer-Fall Proposed Plan for Delta outflow (Figures 1 and 2), Delta outflows would be lower, south Delta exports would be greater, and the low salinity zone further upstream and warmer in the fall (Sep-Oct) of wet years. Such changes would be highly detrimental to salmon and smelt. In below normal years, outflows may be higher from June 20 through August under Alt 4. Such changes would be beneficial to salmon and smelt.

Operation of the SMSCG would lower EC at Collinsville and in Montezuma Slough and increased EC in eastern Suisun Bay. This would be detrimental to smelt rearing in Suisun Bay. For more detail on this issue, see http://calsport.org/fisheriesblog/?p=2813.

Overall, the State’s plan would weaken existing X2 compliance criteria and result in higher exports of water from the south Delta in September and October in wet years. Alternative 4 would potentially provide more summer outflow in below normal years, which currently have no summer ag-salinity standard.

Figure 1. Comparison of Summer-Fall actions for the Proposed Project and Alternative 4.

Figure 2. Proposed Summer-Fall Actions in LTO EIR Alternative 4 (Table 5, p I-2 in EIR).

Figure 3. Collinsville EC in below-normal water year 2016. Salinity (EC) at Collinsville (~km 80) June-Dec 2016, a below normal water year. Red line shows proposed monthly-average EC objective in Alt 4.

Figure 4. Summer water temperature at Rio Vista in northwest Delta in 2016. Note in early summer water temperatures tend to be higher in the lower range of net river flow and high seasonal tides.

Figure 5. Salinity (EC) at Collinsville (~km 80) June-Dec 2018, a below normal water year. Red line shows proposed monthly-average EC objective proposed only in Alt 4.

Figure 6. Salinity (EC) at Collinsville (~km 80) June-Dec 2017, a wet water year. Red line shows proposed monthly-average or 14-day EC objectives in the Proposed Project and Alt 4.

Figure 7. Salinity (EC) at Collinsville (~km 80) June-Dec 2019, a wet water year. Red line shows proposed monthly-average or 14-day EC objectives in the Proposed Project and Alt 4.

 

  1. According to the description in the EIR, Alternative 4 is a more smelt-friendly alternative than the Proposed Project. ↩

Winter 2020 – Salmon need winter flow pulses

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In a February 2019 post, I discussed the importance of winter flows for fall-run salmon in the Central Valley. The peak fry emergence from gravel spawning beds is in winter. Millions of fry move to river margins to await flow pulses to carry them from upper main river and tributary spawning grounds to lower river floodplain, Delta, and Bay nurseries. Without such pulses, the fry stay in the cold rivers competing for limited food and habitat, which leads to poor overall survival and fewer smolts reaching the ocean.

Two January storms in 2020 show the importance of flow pulses for the emigration of fall-run salmon fry (Figures 1-3). Figure 1 shows fry moving downstream from spawning grounds above Red Bluff. Figure 2 shows fry reaching the lower river 100+ miles downstream of Red Bluff. Figure 3 shows fry reaching the north Delta near Sacramento.

What is missing is reservoir releases through tailwater spawning grounds during the storms that create pulses from tributary inflow further downstream. The tributary inflow moves fry downstream from the tributaries. It also moves fry from the mainstem rivers downstream once fry reach the river reaches downstream of the tributaries. But reservoirs capture almost all the flow on the mainstem rivers upstream of the tributaries. During early winter storms, fry aren’t stimulated to move out of the spawning reaches directly downstream of dams.

Figure 4 shows the complete lack of such storage releases in 2020, even after a wet water year when storage was well above average. Pulse flows are needed below all the main storage reservoirs: Shasta, Whiskeytown, Oroville, Folsom, Bullards Bar, Camanche, New Melones, etc. Fry movement from these prime tailwater spawning grounds would then take advantage of the natural rainfall in the main rivers moving through the Delta and on to the Bay nurseries.

Neither of the recent National Marine Fisheries Service’s (NMFS) consultations and the associated biological opinion with Reclamation on the Central Valley Project promotes such winter flow pulses.1 NMFS mandates spring pulses to help smolts (juveniles that are larger and older than fry) reach the Bay. Spring pulses are important, but they are not enough. While individual smolts are more likely to reach the Bay than individual fry, fry vastly outnumber smolts and should contribute substantially to the adult salmon populations. Winter flow pulses are needed because they will improve the survival to adulthood of wild salmon fry.

For more on the importance of increasing the survival rate of wild salmon fry in the Central Valley, see a recent paper by Sturrock et al. 2019. 2

Figure 1. Catch of salmon fry in screw traps and river flow (cfs) in Sacramento River near Red Bluff, January 2020. Data source: http://www.cbr.washington.edu/sacramento/data/juv_monitoring.html


Figure 2. Screw-trap catch rates for salmon fry and river conditions in lower Sacramento River near Colusa and Knights Landing winter 2020. Source: http://www.cbr.washington.edu/sacramento/data/juv_monitoring.html

Figure 3. Trawl and seine catch rates of salmon fry and river conditions in lower Sacramento River in north Delta near Sacramento winter 2020. source: http://www.cbr.washington.edu/sacramento/data/juv_monitoring.html

Figure 4. Winter 2020 flows in rivers and below dams in Central Valley. Lower Sacramento River: Red Bluff (BND), Wilkins Slough (WLK); Delta inflow at Verona (VON), Freeport (FPT). Dam releases to American River (AFO), Feather River (GRL), Stanislaus River (RIP), Sacramento River (KWK), San Joaquin River (VNS). source: http://www.cbr.washington.edu/sacramento/data/

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 ↩

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 ↩