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.

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.

The Importance of the Bay-Delta Estuary to the Recovery of Wild Chinook Salmon

Common sense says salmon recovery efforts should focus on the most important factors that control fish population dynamics. In reviewing Central Valley population dynamics, I have seen each life stage and each individual controlling factor become important at one time or another. In my experience, the estuarine rearing and migrating stage is an essential component that is not given enough attention.

Central Valley salmon populations are nearly all “ocean-type” Chinook salmon, meaning they move to the ocean usually during their first six months of life, with substantial estuary rearing as fry, fingerlings, and pre-smolts. That is not to say that yearling smolts contributions are not important. It is that they are a minor contribution in “ocean-type” Chinook (note that late-fall-run are “river-type”).

I have always believed the survival of wild salmon fry in the Bay-Delta to be a key limiting factor in wild salmon production in the Central Valley. Hatcheries have kept smolt numbers to the ocean up, while the survival of wild salmon eggs, fry, fingerlings, and smolts has worsened. Fry-fingerling estuary survival is important, if only in the sense of sheer numbers and the resulting potential to increase overall smolt production. This is true for fall-run, spring-run, and winter-run populations. There is substantial evidence that returning wild adult salmon are predominantly from the estuarine-reared groups. Such evidence exists from fish surveys, scale analyses, and genetic studies. Thus, a recovery program for wild salmon should include a strong focus on estuarine rearing and survival.

My beliefs are shaped in large part from my personal experiences in conducting winter seine and screw trap surveys throughout the Bay-Delta and lower rivers. Young wild salmon classified as fry and fingerlings, 30-50 mm (1-2 inches), dominate the inshore landscape and screw trap collections. Millions of fry and fingerlings pour out of the spawning rivers and tributaries into the main rivers and into the Delta, where they dominate the winter fish community. Larger, more elusive pre-smolts, mostly winter-run, are also present in smaller numbers, but in numbers important to the winter-run population. Yes, there are millions of fry left to rear in highly regulated and disturbed river habitat, but their overall numbers are fewer, with less potential for ultimate survival to smolts entering the ocean than their estuarine counterparts.

One of the better indicators of the general pattern of estuarine use by salmon is fish salvage collections at the massive federal and state pumping plants in the south Delta. As shown in Figure 1, December is important in the estuary for winter-run and late-fall-run pre-smolts and yearlings, respectively. The January through March period is important for spring-run and fall-run fry/fingerlings. The April through June spring period is important for spring-run and fall-run pre-smolts.

To support juvenile salmon in the estuary, Delta habitat therefore needs protection from December through June. Natural flows and flow direction patterns are important habitat features. Water temperature is important in late spring. Exports affect such habitat, especially in dry, low-flow years.

The State Water Resources Control Board is in the process of revising water quality standards in the Bay-Delta watershed.1 Salinity, flow, water temperature, and export-limit standards need updates to protect salmon using the Bay-Delta through the winter and spring. Such protections will be key to wild salmon recovery in the Central Valley.

Figure 1. Salmon salvage at south Delta pumping plants in 2011. Note red-outlined groups of predominately wild salmon. Blue dots depict salvage events for hatchery salmon.

 

Shasta River Update – April 2019

A February 20, 2019 article in the Eureka Times-Standard reported continuing improvement of Klamath River fall-run Chinook.

“The number of natural area spawners was 53,624 adults, which exceeded the preseason expectation of 40,700. However, the stock is still in “overfished” status as escapement was not met the previous three seasons. The estimated hatchery return was 18,564 adults for the basin.

Spawning escapement to the upper Klamath River tributaries (Salmon, Scott, and Shasta Rivers), where spawning was only minimally affected by hatchery strays, totaled 21,109 adults. The Shasta River has historically been the most important Chinook salmon spawning stream in the upper Klamath River, supporting a spawning escapement of 27,600 adults as recently as 2012 and 63,700 in 1935. The escapement in 2018 to the Shasta River was 18,673 adults. Escapement to the Salmon and Scott Rivers was 1,228 and 1,208 adults, respectively.”

In a May 2017 post, I discussed an increasing contribution to the Klamath run from the Shasta River.  In Figure 1 below, I have updated my original spawner-recruit analysis from the prior post with 2017 and 2018 escapement numbers for the Shasta River.  The Shasta run in fall 2018 was third highest on record for the Shasta River.  The river’s fall-run population continues to benefit from improved water management.  Coho salmon and steelhead have yet to show significant improvements (Figure 2).

An February 26, 2019 article from the publication Grist (posted in 2/26/19 Maven’s Digest) describes changes to water management in the Shasta River.  The Nature Conservancy, using public grant funds, purchased the nearly 5000-acre Shasta Big Springs Ranch for $14 million in 2009.  More recently, the California Department of Fish and Wildlife purchased the water rights of the Shasta Big Springs Ranch.  Now, more water is left in the Shasta River, and only a third (1500 acres) of the ranch remains irrigated.  The article in Grist states that the new allocation of water has negatively affected the ranch’s ability to support wildlife and threatened its ability to support ranching.  In addition, the article questions the benefits of the new management regime to fish: “[T]he fish don’t seem to be doing much better either.”

While some will argue the relative values of ranching and fish protection,  I see no grounds to argue that changes in water management have not been positive to the Shasta River and Klamath River salmon.  Summer flows in the river below the ranch appear to have improved over the long term average (Figure 3).  Many of the Shasta River’s Chinook and Coho salmon spawn in the Big Springs area and in the river below Big Springs, and depend on flow and cold water input from the springs.  Even with the contribution of this flow, water temperatures are marginal (>65oF) for young salmon from May to September (Figure 4).

From my perspective, the loss of several thousand acres of irrigated pasture out of roughly 25,000 acres in the Shasta Valley seems a small price to pay for a large step towards the recovery of Shasta and Klamath River salmon.

Figure 1. Spawner-recruit relationship for Shasta River. Escapement estimates (log10X – 2 transformed) are plotted for recruits by escapement (spawners) three years earlier. Year shown is recruit (escapement) year. The number is the year that fish returned to the Shasta River to spawn. The color of the number depicts the water-year type in the Shasta River during the year the recruits reared. The color of the circle depicts the water-year type in the Klamath River during the year the recruits reared. Blue is for Wet water-year types. Green is for Normal water-year types. Red is for Dry water-year types. Example: 90 depicts fish that returned to the Shasta River as adult spawners in 1990. These fish were spawned in 1987 and reared in winter-spring 1988. The red number shows that the 1988 rearing year was a Dry water year in the Shasta River; the red circle shows that the 1988 rearing year was a Dry water year in the Klamath River. Note very poor recruits per spawner in 1990-1993 drought period, compared with relatively high recruits per spawner from 2011-2018, even though the latter period included the 2012-2016 drought.

Figure 2. Shasta River salmonid runs from 1930 to 2017. Source: https://www.casalmon.org/salmon-snapshots/history/shasta-river

Figure 3. Shasta River flows in the Shasta River below Big Springs 2016-2018 with 30 year average. Note summer base flow appears to have improved by approximately 10-30 cfs.

Figure 4. Water temperature in the Shasta River below Big Springs including summers of 2017 and 2018. Source: DWR CDEC.