Category Archives: Bay-Delta

“Robust” San Joaquin Salmon Runs

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The San Joaquin River appears to be seeing a boon in salmon runs this year despite the recent drought. Editor Dennis Wyatt of the Manteca Bulletin suggested on December 14 that “robust” salmon runs on the San Joaquin River in recent years “discredit” state claims that more of unimpaired flow of the Stanislaus, Tuolumne, and Merced rivers should be passed to the Bay-Delta:

Spawning adult numbers after being in the 1,000 to 2,000 range from 2006 through 2011 now consistently surpass 5,000 despite the drought. The scientific research conducted by FISHBIO over the past decade and underwritten by the South San Joaquin Irrigation District and Oakdale Irrigation District is being used by the two water agencies to discredit state claims that the only way to increase salmon on the Stanislaus River — and the neighboring Tuolumne and Merced rivers — is by ratcheting up unimpaired flows to 40 percent between February and June. 1

This theory is circulating among supporters of water purveyors who draw water from the Stanislaus. For example, Mr. Wyatt’s editorial was reproduced verbatim on Congressman Jeff Denham’s website.2

One of the main reasons for the recent decade of run increases is most likely increases in flow requirements in the spring and fall as mandated in the National Marine Fisheries Service’s 2009/2011 biological opinion for the Central Valley Project. It is more logical that further flow improvements would lead to further salmon enhancements, perhaps even approaching target levels specified in the Central Valley Project Improvement Act of 1992 (CVPIA).

There is a long way to go. The so-called robust runs are far below the CVPIA target of 78,000 salmon for the San Joaquin, numbers that were most recently achieved in Water Year 2000 (Figure 1). While there have been improvements during the last ten years, eight of which were drought years (Figure 2), runs are still about 70,000 fish short of the doubling goal.

In addition, much of the recent improvement is related to increased hatchery production from the state hatcheries on the Mokelumne and Merced rivers (Figure 3). Hatchery production also benefits from trucking hatchery smolts to the Bay. Runs in the Stanislaus and Tuolumne also benefit from strays from the two hatcheries. The CVPIA doubling goal is for natural production.

Finally, there needs to be defined fall flow pulses in addition to higher spring flows. Fall pulse flows reduce water temperature in the three tributaries and mainstem during the fall migration period. In the past, drought year fall flows were depressed (Figure 4). This made it harder for fish to find the San Joaquin tributaries and led to high fall water temperatures (Figure 5). High temperatures can block or hinder adult salmon migration, reduce adult pre-spawn survival, and lower egg viability. Lack of fall flow pulses in 2014 and 2015 led to poor salmon escapement, especially in the Tuolumne and Merced Rivers. Higher flows and lower water temperatures in the Stanislaus in 2015 likely led to a greater proportion of the overall San Joaquin run choosing the Stanislaus River (Figure 2). Fall flows from tributary reservoirs should be sufficient to maintain tributary water temperature below 60°F and San Joaquin River temperatures below 65°F. These goals are achievable in most water years, and were for the most part achieved in the San Joaquin River in October, 2016 (Figure 5).

Sorry, folks. Flow matters.

Figure 1. San Joaquin salmon production 1957-2010 as related to flow two years earlier. Source: Appendix C, SWRCB 2012.

Figure 1. San Joaquin salmon production 1957-2010 as related to flow two years earlier. Source: Appendix C, SWRCB 2012.

Figure 2. Salmon run totals (escapement) from the Stanislaus, Tuolumne, and Merced rivers 2005-2015. Data source: CDFW.

Figure 2. Salmon run totals (escapement) from the Stanislaus, Tuolumne, and Merced rivers 2005-2015. Data source: CDFW.

Figure 3. San Joaquin salmon escapement from 2008 to 2015. Source: CDFW.

Figure 3. San Joaquin salmon escapement from 2008 to 2015. Source: CDFW.

Figure 4. San Joaquin River flow 2003-2016 at Vernalis (downstream of confluence with Stanislaus, Tuolumne, and Merced rivers). Red circles denote drought years lacking adequate fall flow prescriptions.

Figure 4. San Joaquin River flow 2003-2016 at Vernalis (downstream of confluence with Stanislaus, Tuolumne, and Merced rivers). Red circles denote drought years lacking adequate fall flow prescriptions.

Figure 5. Fall water temperature of San Joaquin River at Vernalis in 2015 (top) and 2016 (bottom). Red circles denotes key salmon migration period when fall flow prescriptions occur. Note higher water temperature in 2015 compared to 2016, which had higher fall flows. Source: CDEC.

Figure 5. Fall water temperature of San Joaquin River at Vernalis in 2015 (top) and 2016 (bottom). Red circles denotes key salmon migration period when fall flow prescriptions occur. Note higher water temperature in 2015 compared to 2016, which had higher fall flows. Source: CDEC.

Department of Interior’s Central Valley Anadromous Fish Habitat Restoration Program

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CVPIA 2017 Annual Work Plan Draft Cover Art

Over the past twenty-plus years, the US Bureau of Reclamation and the US Fish and Wildlife Service have implemented multiple actions to restore physical habitat for salmon and steelhead in the Central Valley.  While these agencies in the Department of Interior have focused much of their efforts on the tailwaters of Reclamation’s federal Central Valley Project dams (Shasta/Keswick, Whiskeytown, Folsom/Nimbus, and New Melones), they have implemented projects on other tributaries as well (e.g., Butte Creek).

The overall mandate and effort stems from the Central Valley Project Improvement Act (CVPIA) of 1992 and its sub-element – the Anadromous Fish Restoration Program (AFRP).  The Act established the Central Valley Project Restoration Fund (CVPRF or Restoration Fund), which includes the Trinity River Restoration Plan and the San Joaquin River Restoration Plan.  Funding comes from appropriations from the U.S. Congress, collections from water and power contractors, and non-federal cost-share obligations.  Funding varies annually – the federal share for 2017 projects is budgeted at $22 million.1  Total funding for Interior’s 2017 efforts in the proposed federal budget is approximately $55 million.  Major projects for 2017 include stream channel restorations and fish passage projects throughout the Central Valley.

With the changes that will come with the new federal government administration in 2017, we can expect many changes to the program, including funding.  Setting priorities and funding allocation for the coming year will be a complex process.  The state and federal goals and objectives may be in conflict.  The 2017 and coming years’ programs will help determine the future of Central Valley salmon, steelhead, sturgeon, American shad, and striped bass.

Commercial and sport fishermen will have to be especially vigilant.  The whole restoration process has so many components that often are uncoordinated.  Resource advocates should seek a stronger role in the process and come together in common purpose.  Let’s start by having a strong voice in the future of CVPRF and CVPIA-AFRP.

Another Chance for Delta Smelt – 2017 Comeback?

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In 2010 Delta smelt started a two-year comeback after three years of drought.  The fourth lowest fall index on record (2009) brought a modest increase in the normal water year 2010 summer and fall indices that in turn led to the modest 2011 wet year recovery.  Another comeback may be in the making with the wet fall-winter of water year 2017.  After the record low 2015 summer and fall indices, and what were perceived to be record lows in 2016, the remaining smelt seem to be making a run of it this wet fall-winter as they did in 2010 (Figures 1 and 2).  In 2010 exports were constrained by the 2009 Smelt Biological Opinion (BO) limits on OMR of -5000 cfs or below (Figure 3).  Only one Delta smelt was observed in December and January at the south Delta fish salvage facilities that year (most likely due to the export restrictions).  So far this year prescribed export restrictions and recommendations from the Smelt Working Group on OMR flows per the BO have been ignored, in part due to relaxations allowed in the new water bill the President signed last week.  Exports and negative OMR flows remain high (Figure 4).  With such high winter exports and associated highly negative OMR flows, it remains to be seen if salvage numbers remain low (none so far) and a comeback occurs in 2017.

Figure 1. Delta smelt distribution in January 2010 Kodiak Trawl Survey 2010. Source: CDFW.

Figure 1. Delta smelt distribution in January 2010 Kodiak Trawl Survey. Source: CDFW.

Figure 2. Delta smelt distribution in December 2016 Kodiak Trawl Survey. Source: CDFW.

Figure 2. Delta smelt distribution in December 2016 Kodiak Trawl Survey. Source: CDFW.

Figure 3. Old and Middle River net flow in the central Delta downstream of the South Delta export pumps 12/2/2009-1/28/2010. Negative flows are caused by reverse flows in these river channels toward the pumping facilities. Source: CDEC.

Figure 3. Old and Middle River net flow in the central Delta downstream of the South Delta export pumps 12/2/2009-1/28/2010. Negative flows are caused by reverse flows in these river channels toward the pumping facilities. Source: CDEC.

Figure 4. Old and Middle River net flow in the central Delta downstream of the South Delta export pumps 11/21/2016-12/21/2016. Negative flows are caused by reverse flows in these river channels toward the pumping facilities. Source: CDEC.

Figure 4. Old and Middle River net flow in the central Delta downstream of the South Delta export pumps 11/21/2016-12/21/2016. Negative flows are caused by reverse flows in these river channels toward the pumping facilities. Source: CDEC.

Feinstein’s “Poison Pill” for Salmon and Smelt

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Senator Feinstein has added a rider to the Drought Water Bill that has been referred to as a “poison pill” for endangered salmon and smelt. Senator Boxer has vowed to fight passage of the Water Bill because of Feinstein’s “poison pill” rider. Senator Feinstein has claimed that the rider is a compromise to get support for the overall water bill that includes provisions to enhance California’s water supply infrastructure.

“Even amid heavy storms, only 852,000 of the 5.5 million acre-feet of water that flowed into the Delta during the first two months of this year—enough to sustain nearly two million acres of farm land—was sent south. The rest drained into the San Francisco Bay due to a lack of surface storage in the Sierras and pumping restrictions ostensibly intended to protect endangered species…. The Feinstein rider would give regulators some discretion to increase pumping to a little less than half of capacity.” Wall Street Journal article.

Senator Feinstein’s rider would allow weakening of provisions in the federal salmon and smelt biological opinions that restrict Delta export pumping from December to June (Figure 1). The rider would allow more Delta export pumping during periods of higher Delta outflow, as in the two storm periods shown in Figure 1 (bottom chart). Even if this weakening only allowed increased exports up to 50% of capacity, exports could be raised to approximately 13,000 acre-ft per day from the present 2500 to 10,000 acre-feet per day limits under the biological opinions (the amounts vary with the immediate risk to species). These risks would be substantial and would further jeopardize winter-run salmon, spring-run salmon, green sturgeon, steelhead, Delta smelt, and longfin smelt. All of these species depend heavily on the Bay-Delta during the times of year in which the current biological opinions potentially restrict exports.

Figure 1. Delta export pumping (top) and Delta outflow (bottom) in Water Year 2016.

Figure 1. Delta export pumping (top) and Delta outflow (bottom) in Water Year 2016.

Suisun Bay Marsh Habitat

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Wet years have led to high production of salmon, steelhead, smelt, sturgeon, splittail, shad, and striped bass in the Central Valley and Bay-Delta. One of main reasons for this high production is that Suisun Bay and Marsh habitat come into play in winter and spring when freshwater dominates the area under high Delta outflows.

High flows from winter-spring storms carry the young of these species from rivers and the Delta into the Bay. Longfin and Delta smelt even spawn in the Bay and adjacent Napa River. In my own personal experience1 surveying the area in winter-spring of the wet years 1978 and 2006, I observed very high use by young of these species, indicating the area’s high importance as a rearing area for estuarine and anadromous fishes. My experience mirrors that of 35 years of study in the Marsh by Peter Moyle at UC Davis.2

Even in dry years, moderate winter Delta outflow from infrequent winter storms pushes freshwater and young anadromous and estuarine fishes into Suisun Bay/Marsh. Rearing in the Bay and Marsh favors survival of juvenile fish for many reasons, chief among them shallow turbid freshwater that provides abundant food, cool waters through spring, and protection from predators. Fish in the Bay and Marsh also have greatly reduced risk of being lost in the interior Delta to poor habitat, abundant predators, the export pumps, and other water diversions.

Once young fish get to the Bay, they grow quickly and become gradually more tolerant of brackish waters that return after the storms. Salmon, steelhead, longfin smelt, and sturgeon make a full transition and move to the lower Bay and ocean. The Delta smelt, splittail, and striped bass remain in the brackish water through the summer and fall, taking advantage of abundant food and the cooler waters of the Bay. No other region offers these advantages and necessary habitat conditions to the anadromous and estuarine fish species of the Central Valley and Bay-Delta.

Efforts have been ongoing for several decades to restore habitat in Suisun Bay-Marsh. Most recently, the restoration has come under the wing of the State Resources Agency’s EcoRestore program with several new projects, most notably the Tule Red project along the north shore of Grizzly Bay (Figure 1). Other potential sites include Wheeler Island, Chipps Island, and Winter Island, in part by including existing duck hunting clubs under active management. These three sites should be actively pursued by EcoRestore, because they could be restored to tidal marsh. Under existing conditions, their low levees are often overtopped during high winter tides in storm surges, allowing young salmon to enter. However, these fish become trapped when water levels drop. Opening these habitats to the tide would provide new habitat and eliminate stranding.

Figure 2 shows a flooded Wheeler Island. The Collinsville area offers many restoration options including Montezuma Island, the old Navy base, and the old PG&E power plant site. Managed wetland areas adjacent to Montezuma Slough within the Marsh offer many opportunities for tidal habitats along the slough (Figure 3). Among all the above opportunities, only Tule Red is included in EcoRestore (Figure 4). EcoRestore should take greater advantage of the existing high value of Suisun Bay-Marsh habitats and the high potential benefits per unit cost of projects in this area compared to other planned projects upstream in the Delta and Valley.

Returning to where this article started, fish need the winter and spring flows to get them to Suisun Bay-Marsh and to sustain them. Even the driest years have winter storms that partly accomplish this despite the capture of most dry year the rain and snowmelt in Valley reservoirs. Thus, dry year storm pulses become so essential. The state and federal water projects in the Delta also covet these storm pulses and divert significant parts of them through the Delta pumps. The proposed Twin Tunnels would take even bigger bites out of dry year storm pulses3 before they are “lost” to the Bay and ocean. Instead, storm pulses should be enhanced in drier years by allowing a reasonable amount of Valley reservoir inflows to pass through the reservoirs and by limiting diversions of storm pulses from the Delta.

Figure 1. Recommended restoration sites in Suisun Bay. CSPA owns 14 acres along the shoreline near Collinsville below the number 6. (Basemap Source: Suisun Marsh Plan)

Figure 1. Recommended restoration sites in Suisun Bay. CSPA owns 14 acres along the shoreline near Collinsville below the number 6. (Basemap Source: Suisun Marsh Plan)

Figure 2. Flooded Wheeler Island on north shore of Honker Bay. Island levees breached in 2005 and have been marginally repaired. Without active management such sites may become permanently breached and actively eroded. See Figure 1 for location. (Source: GoogleEarth)

Figure 2. Flooded Wheeler Island on north shore of Honker Bay. Island levees breached in 2005 and have been marginally repaired. Without active management such sites may become permanently breached and actively eroded. See Figure 1 for location. (Source: GoogleEarth)

Figure 3. Habitat map of Suisun Bay/Marsh. (Source: Suisun Marsh Plan)

Figure 3. Habitat map of Suisun Bay/Marsh. (Source: Suisun Marsh Plan)

Figure 4. EcoRestore projects. (Source: http://resources.ca.gov/ecorestore/ )

Figure 4. EcoRestore projects. (Source: http://resources.ca.gov/ecorestore/ )

 

  1. Cannon, T. and T. Kennedy, 2007. Fish Use of Shallow Water Habitats of the Western Delta 1978-79 and 2002-07, May 2007. ↩
  2. https://californiawaterblog.com/2011/07/28/the-future-of-suisun-marsh/ ↩
  3. The Tunnel proposal does recognize the importance of the storm pulses for the Bay and would allow some of the first pulse to pass. ↩