Survival to Adulthood of American River Hatchery Salmon

The Nimbus Fish Hatchery on the American River produces approximately 4 million fall-run Chinook salmon smolts each year for release to the American River and to San Pablo Bay (after being held there in net pens). Releases are made from late April to early June. Release return rates are available for 2007-2015.1 In 2014 and 2015, all releases were to the Bay. From 2016 to 2018, a substantial proportion of releases were to the American River.

Return rates (percent captured as adults in fisheries plus percent returning as adults to spawning grounds and the hatchery) from 2007 to 2015 releases varied from 0.3 to 3.7 percent (Figure 1). Return rates were higher for wet year 2011 and normal years 2010 and 2012. Return rates for river and Bay release groups were similar in wetter years. Overall return rates in dry years were lower than return rates in wetter years, with higher returns for Bay release groups than for river release groups.

River return rates were low in years with lower flow and higher water temperature in the lower American River. American River flow was lower in late spring 2009 and 2013 (Figure 2). River temperatures were higher (>55oF) in these drier years (Figure 3), as were Delta temperatures (>68oF; Figure 4). Such conditions are detrimental to smolt survival.

Poor returns (<1%) from dry year Bay releases (<1000 cfs Delta outflow) are associated with low Delta outflows (<10,000 cfs, Figure 5). Lower ocean survival may have also contributed to poorer Bay release returns.

Conclusions and Recommendations

An optimal strategy for increasing the contribution of Nimbus Hatchery’s 4 million fall-run Chinook salmon smolts would be:

  1. Release smolts in the American River in wetter years with higher river flow and lower river water temperature.
  2. Release smolts in the Bay in dry years; do not release in river.
  3. Maintain Delta outflows above 10,000 cfs during periods of release of smolts to the Bay.

This strategy could increase hatchery smolt returns as much as 1%, or by 40,000 adult salmon, assuming 4 million smolts. In drier years, this would double or triple the contribution from the American River hatchery to salmon available for catch and to salmon returning to the American River to spawn.

Figure 1. Return rates for Nimbus Hatchery smolt late spring releases to the American River (red dots) and San Pablo Bay (black color dots).

Figure 2. Lower American River flows 2009-2013. Red dots indicate periods of release of hatchery smolts to the river.

Figure 3. Water temperatures in the lower American River from 2009 to 2015. Red dots indicate periods of release of hatchery smolts to the river.

Figure 4. Water temperatures in the north Delta 2009 to 2015. Red dots indicate periods of release of hatchery smolts to the river.

Figure 5. Delta outflows 2007-2015. Red circles indicate periods of release of hatchery smolts to the Bay.

Winter Trawl Survey – Delta Smelt 2019 Adult Spawning Run Update

A January 2, 2019 California Department of Fish and Wildlife (CDFW) memo relates that the fall midwater trawl index for Delta smelt was zero (none collected), though an attachment from the U.S. Fish and Wildlife Service (USFWS) shows that some Delta smelt were captured in late 2018 in non-index locations, as was the case in other recent years. The CDFW memo also relates that 5 smelt were captured in the December Kodiak Trawl Survey.

In an effort to update my last winter trawl post, April 2018, I present the winter survey results from 2002 through 2019 in the figure below. The 2018 and 2019 winter indices are consistent with the fall and summer surveys.

The fact that some Delta smelt remain in the Bay-Delta indicates that it might not be too late to save them from extinction, especially with hatchery supplementation. However, there has been no public description of CDFW’s or USFWS’s plan for Delta smelt recovery in 2019-2020. The present recovery plan for Delta smelt is dated 1996. USFWS should update the Delta smelt recovery plan immediately, and USFWS and CDFW should implement it. The State Water Resources Control Board’s effort to update Delta water quality standards should also include measures to recover smelt.

Chart of winter smelt survey results from 2002 through 2019

Improved Yolo Bypass Fish Passage

Some salmon and sturgeon adults migrating up the Sacramento River this spring have had new help in passing upstream via the Yolo Bypass. With roughly half the Sacramento River’s flood waters flowing through the Yolo Bypass at the beginning of March, many salmon and sturgeon returning to the upper river to spawn likely chose entered the lower end of the Bypass at Rio Vista. These fish had a new notch opening to help them get over the Fremont Weir at the upper end of the 40-mile-long Bypass (Figure 1) and back into the Sacramento River to continue their journey.

The new $6-million gated-notch opening in the Fremont Weir is the first of several to be built into the two-mile-wide weir to help fish passage. The notches will allow an easier passage route over the weir, especially for large sturgeon. The notches are especially important in allowing an extended period for adult fish to finish their passage through the Bypass when Sacramento River water levels fall and the river flow ceases spilling over the weir into the Bypass. In the past, these conditions would have trapped any fish that remained in the Bypass. The notches will also help pass downstream-migrating juvenile salmon to enter the Yolo Bypass, where there is potential beneficial tidal and floodplain rearing habitat.

The first year of the new notch’s operation has not been without some glitches.1 Significant numbers of salmon and sturgeon have died and probably continue to die at the weir and in the Bypass.

But the new notch was not the underlying cause of this problem. The problem lies in flood control and reservoir storage management in the Central Valley. Drastic reductions in river flow and water levels led to fish stranding in the Bypass, the draining of the floodplain, and a rapid rise in water temperatures in the Bypass that stressed migrating fish.

  1. Shasta/Keswick reservoir releases were reduced sharply after two major flood releases this winter/spring (Figure 2).
  2. This led to abrupt ends to Fremont Weir overflows into the Yolo Bypass (Figure 3)
  3. The sharp drops in water levels in the river allowed only one week of extended Bypass inflows through the new notch (Figure 4).
  4. That led to a rapid draining of the Bypass (Figures 5 and 6).
  5. This in turn led to excessive water temperatures in the Bypass (Figure 7) for migrating and rearing salmon (>70oF).

For the new notches to be effective, an extended period of flow through the new notches will be needed to allow time for migrating and rearing salmon and sturgeon to safely exit the Yolo Bypass without being subjected to a sudden draining of warm water from the shallow margins of the Bypass. With a near record snowpack and filling reservoirs, there were sufficient river flows and reservoir storage this year to extend the duration of river flows into the Yolo Bypass.

Figure 1. New Fremont Weir gated notch to help fish passage between Yolo Bypass and Sacramento River.

Figure 1. New Fremont Weir gated notch to help fish passage between Yolo Bypass and Sacramento River.

Figure 2. Reservoir releases from Shasta/Keswick dams in winter-spring 2019.

Figure 2. Reservoir releases from Shasta/Keswick dams in winter-spring 2019.

Figure 3. Flow into Yolo Bypass from Sacramento River at Fremont Weir in winter-spring 2019.

Figure 3. Flow into Yolo Bypass from Sacramento River at Fremont Weir in winter-spring 2019.

Figure 4. Water elevation of Sacramento River at Fremont Weir in winter-spring 2019. Top of weir is at 32-ft elevation. Bottom of new notch is at 25-ft elevation. Extended operation of new notch would have occurred from April 22-28.

Figure 4. Water elevation of Sacramento River at Fremont Weir in winter-spring 2019. Top of weir is at 32-ft elevation. Bottom of new notch is at 25-ft elevation. Extended operation of new notch would have occurred from April 22-28.

Figure 5. Flow in upper Yolo Bypass in winter-spring 2019.

Figure 5. Flow in upper Yolo Bypass in winter-spring 2019.

Figure 6. Water elevation in mid Yolo Bypass during Bypass draining in last week of April 2019.

Figure 6. Water elevation in mid Yolo Bypass during Bypass draining in last week of April 2019.

Figure 7. Water temperature in mid Yolo Bypass at Lisbon Weir during Bypass draining in last week of April 2019.

Figure 7. Water temperature in mid Yolo Bypass at Lisbon Weir during Bypass draining in last week of April 2019.

 

South Delta Salmon Trap

Unless there are high Delta inflows, south Delta export pumping creates a hydrologic “trap” for emigrating salmon and other Delta fishes. Even under moderate Delta inflows and outflows, as occurred in January 2019 (Figure 1), south Delta pumping traps salmon emigrating from both the Sacramento and San Joaquin river systems. This is because the pumps trap nearly all the water from the San Joaquin and about a third of the Sacramento River water the latter primarily via cross-Delta flow in Georgianna Slough (GS). In contrast, under high flows, the trap is confined only to the immediate area of the south Delta export pumps (Figure 2).

Susceptibility to the “trap” for Sacramento salmon under moderate early winter Delta flows is evident from the collection of smolts from the Coleman fish hatchery at south Delta fish salvage facilities (Figure 3, blue and green dots). Susceptibility of San Joaquin salmon smolts under moderate and high flows is evident from San Joaquin hatchery smolts salvage (Figure 3, orange dots).

Lower export limits in winter-spring since 2009 have helped to minimize the frequency of conditions in which salmon become trapped in the south Delta. Exports and salmon salvage are 30-50 % lower than pre-2009 levels, and sometimes lower still. However, political forces may eliminate these export restrictions and greatly increase the trapping of salmon in the south Delta. This would further limit the potential for salmon recovery in the Central Valley.

The State Water Board’s ongoing process of setting new Delta water quality standards should adopt more stringent measures to minimize the trapping of salmon in the south Delta. Such measures should include further restrictions on exports and increased flows in the lower San Joaquin River. Other options include:

  1. Constructing a barrier or fish screen at the head of Old River;
  2. Opening the Delta Cross Channel to increase net downstream flows in the lower San Joaquin channel within the Delta; and
  3. Increasing Delta outflow.

Figure 1. Delta hydrology 1-15-19. Red arrows denote negative or upstream flows. SR = Sac River. JPT = Jersey Point. GS = Georgianna Sl. MOK = Mokelumne River. DS and FR = Dutch Sl and False River. PPT = Prisoners Pt. OMR = Old and Middle Rivers.

 

Figure 2. Delta hydrology 3-15-19. Red arrows denote negative or upstream flows. SR = Sac River. JPT = Jersey Point. GS = Georgianna Sl. DS and FR = Dutch Sl and False River. PPT = Prisoners Pt. OMR = Old and Middle Rivers.

Figure 3. Salmon salvage in winter-spring 2019. Colored dots represent specific hatchery release groups noted by date of release along top margin of chart. River and Delta flows and exports (SWP+CVP) are shown in bottom chart.

Dutch Slough Tidal Marsh Restoration

The Dutch Slough Tidal Restoration Project,1 newly redesigned (Figure 1), has some improved design elements, but remains flawed and potentially detrimental to Delta native fishes. Unless the flaws are overcome, the project will be a huge waste of limited Delta restoration funds.

First, the proposed project’s location within the Delta (Figure 2) is extremely detrimental.

  1. The location is an eastward extension of Big Break, an open water of the west Delta that is infested with non-native invasive aquatic plants and that breeds non-native fishes.
  2. The project is located on Dutch Slough, detrimentally warm in summer (Figure 3), with net flows that are negative and eastward toward the south Delta export pumps (Figure 4).

Second, and equally important, the project as designed would further contribute to the existing detrimental non-native vegetation and warm water problems.

  1. The extensive new dead-end slough complexes will become infested with invasive plants and will contribute to lowering turbidity and warming.
  2. The new subtidal habitat will further add to that in Big Break with more invasive plants and breeding and rearing habitat for non-native fish.

Third, the new habitat will attract breeding smelt and rearing juvenile salmon into an area where their eventual survival is highly questionable.

Can design changes overcome these flaws? Yes, but only in combination with other regional fixes.

  1. Big Break must first be restored along the lines being considered and studied in the Franks Tract Restoration Feasibility Study.
  2. A tide gate must be installed on east Dutch Slough, similar to that being considered for False River in the Franks Tract restoration. (This would fix the negative net flows toward south Delta exports and reduce salinity intrusion.)
  3. Open-water subtidal habitat should be eliminated. (Make the subtidal element diked-off non-tidal marsh.)
  4. Dead-end sloughs should allow flow-through to increase tidal circulation.
  5. Finally, more freshwater outflow should be allocated by reducing south Delta exports in low outflow conditions, in order to reduce salinity intrusion.

Figure 1. Conceptual design of Dutch Slough restoration project.

Figure 2. Location of Dutch Slough Project in the Delta.

Figure 3. Water temperature in Dutch Slough in 2014 and 2015.

Figure 4. Daily net flows in Dutch Slough 2007-2018.