Wet Winter-Spring 2019 Good for Central Valley Salmon

Posted on June 2, 2019 by Tom Cannon

On May 8, 2019, the California Department of Fish and Wildlife (CDFW) released one million fall-run salmon smolts from the Feather River Fish Hatchery into the lower Feather River.¹ Their prognosis is good, as it is for most salmon, both hatchery and wild, in the Central Valley in this very wet year.

This post focuses on features of wet years that are good for salmon, and how those features help us to understand how to improve salmon production in general. In the past, I have posted a lot about increasing hatchery contributions. In this post, I focus on wild salmon in wet year 2019.

Two periods in early life stage wild salmon survival stand out: fry and smolt migrations. The two periods are well represented in vulnerability to south Delta exports, as seen in intake screen salvage numbers (Figure 1). Fry emerge from river gravels in winter. Many ride the winter flows in February and early March into the tidal Bay-Delta, where they rear for a month or two before heading to the ocean as smolts. From April to June, smolts are migrating from rivers, Delta, and Bay to the ocean. This focused two-migration-period pattern can also be seen in lower river, upper Delta, and upper Bay fish surveys (Figures 2-5). Note that fry are not apparent in the Bay trawls (Figure 5), because fry concentrate in shallow margins that trawls cannot sample. Flows support migrations: getting fry to the Bay-Delta and sustaining smolts to the ocean.

So what factors appear important?

January-February flow pulses that carry fry to Bay-Delta rearing habitats.
May-June smolt migration Delta inflows and outflows, and water temperatures.

Without winter flow pulses, fry cannot reach the Bay-Delta. Without adequate flows and cool water temperatures (<20^oC, 68^oF) in spring, smolt survival to the ocean is poor. Even in this very wet year, May conditions are becoming marginal in the lower Sacramento River for migrating smolts (Figures 2 and 3). Delta and Bay conditions remain near optimal (Figures 4 and 5) because of major snow-melt flow contributions from Feather-Yuba and American rivers.

Figure 1. South Delta pumping plant fish salvage sampling surveys (salmon only) in winter-spring 2019. Hatchery smolts dominate salvage except during wild fry and smolt migration periods.

Figure 2. Trap catch of juvenile salmon at Tisdale Weir (river mile 120) winter-spring 2019.

Figure 3. Trap catch of juvenile salmon at Knights Landing (river mile 90) winter-spring 2019. Note Knights Landing is upstream of mouth of Feather River. Flows are much reduced in early May, and water temperatures have reached the stressful level of 20^oC.

Figure 4. Trawl catch of juvenile salmon at Sacramento (river mile 50) winter-spring 2019. Note high flow of 30,000 cfs in early May from major contributions from Feather-Yuba and American rivers.

Figure 5. Trawl catch of juvenile salmon at Chipps Island near Antioch in Suisun Bay winter-spring 2019.

https://cdfgnews.wordpress.com/2019/05/08/feather-river-smolt-release-to-help-biologists-study-salmon-life-cycle/ ↩

Brood Years 2011-2013 Feather Hatchery Survival to Adulthood What was learned?

Posted on May 27, 2019 by Tom Cannon

The number of fall-run salmon released from the Feather River Fish Hatchery that are either captured in fisheries or that return to the Feather River as adults (% survival) varies from year to year and within each year.¹ Recent patterns of survival to adulthood from brood years 2011-2013 provide insights into the effectiveness and potential success of different strategies for releasing smolts from the hatchery.

Brood Year 2011

DFW released nearly 7 million 2011 brood year smolts in spring 2012. Survival improved as fish were released with later in the season, with highest survival for late-released older smolts on the coast at Half Moon Bay (Figure 1). The declining late spring survival for the San Pablo Bay releases may be related to low late spring Delta Outflow in this below-normal water year (Figure 2). The late-season Half Moon Bay release group had a 5% rate of survival (Table 1), as compared to about 2% for late season releases from San Pablo Bay (North-East San Francisco Bay). Approximately three-quarters of survival to adulthood was accounted for in reports of fish captured, with the remainder from counts at spawning grounds and hatcheries.

Brood Year 2012

From the approximately 6.5 million Feather hatchery smolts of brood year 2012 released in spring of drought year 2013, Golden Gate releases had the highest survival rates at near 4% (Figure 3). Lower Sacramento River releases had poor success, with a survival rate to adulthood of less than 0.1%. This poor outcome is likely a consequence of low flow and high water temperatures in the river (Figures 4 and 5). Bay releases had relatively good returns of approximately 1.4-2.3% under relatively good Delta outflow conditions.

Brood Year 2013

Among the approximately 6.5 million Feather hatchery smolts of brood year 2013 released in spring of critical drought year 2014, most groups survived poorly (<1%; Figure 7). The group released to Half Moon Bay on the coast was an exception at 3.3%. One group released in San Pablo Bay on April 29 had a modest survival rate of 1.3%; their release occurred during a period of slightly higher Delta outflow (8000-9000 cfs; Figure 8). Other groups released to Bay or Delta had low survival; their release occurred under very low Delta outflow (3000-5000 cfs).

Straying

The most commonly stated concern for trucking and barging smolts to the Delta, Bay, Golden Gate, and coastal bays is straying of adult spawners to other rivers and hatcheries.

The highest performing groups, HMBay releases, had the highest risk of straying being trucked to the coast outside the Golden Gate. Of the BY 2011 group’s (Table 1, Figure 1) hatchery returns, 534 (90%) were to its origin hatchery on the Feather River. This compares with the 91% return for corresponding release to San Pablo Bay net pens. This compares to 96% for the FR group.
Golden Gate releases had similar straying rates. For BY 2012 (Figure 3), trucked smolts had 92% of hatchery returns to the origin hatchery, while barged fish had 93% return. These rates compare to 81% of hatchery returns to origin hatchery for the 5/23 SPB net pen group. Only two fish returned to Central Valley hatcheries (both to Feather River Hatchery) from the BY 2012 FRiv group.

Summary

The rate of survival to adulthood of hatchery release groups was higher in wetter years.
Early spring (prior to mid April) smolt releases had lower survival rates than later spring releases.
Survival of smolts released in-river was modest in wetter years and very poor in dry years.
Highest rates of survival (4-5%) were from Half Moon Bay on the coast south of San Francisco.
San Pablo Bay pen release return rates were better (2-3%) under higher Delta outflow; returns were poorer (<1%) when San Pablo releases occurred during periods of low Delta outflow (3000-5000 cfs).
Straying rates overall were generally low (5-10%). The lowest straying rate (4%) was from river release at mouth of Feather River.

Conclusions

Coastal and Golden Gate smolt releases provide the highest rates of survival to adulthood. Stray rates for these release groups are low. Rates of survival for smolts released in-river and in San Pablo Bay are poor in drier years with low Delta outflow.

The best strategy for high rates of survival would appear to be to make most or all releases in drier years at the coast and the Golden Gate, and to make releases in wetter years in-river and in San Pablo Bay. Releases of smolts to the rivers in dry years and in years with poor Delta outflow should be avoided, especially during late spring when flows are low and water temperatures are high.
Table 1. Returns from Tag Group 060374 released at Half Moon Bay.

Figure 1. Survival rates for brood year 2011 Feather River Hatchery smolts released in spring 2012. GG is Golden Gate. SPB is San Pablo Bay. FR is Feather River. HMBay is Half Moon Bay along the coast south of San Francisco.

Figure 2. Delta outflow in spring 2012.

Figure 3. Survival rates for brood year 2012 Feather River Hatchery smolts released in spring 2013. GG is Golden Gate. SPBNP is San Pablo Bay net pen. FRiv is Sacramento River below mouth of Feather River. HMBay is Half Moon Bay. SCruz is Santa Cruz harbor.

Figure 4. Sacramento River flow below mouth of the Feather River in spring 2013, along with historical average. Note lower than average flow in April and early May.

Figure 5. Sacramento River water temperatures below mouth of the Feather River in spring 2013, along with historical average. Note that water temperatures in spring 2013 were about 5oC above the long-term average through early June.

Figure 6. Delta outflow in spring 2013.

Figure 7. Survival rates for brood year 2013 Feather River Hatchery smolts released in spring 2014. GG is Golden Gate. SPBNP is San Pablo Bay net pen. Rio Vista is North Delta. HMBay is Half Moon Bay.

Figure 8. Delta outflow in spring 2014.

http://calsport.org/fisheriesblog/?p=1867 ↩

Survival to Adulthood of American River Hatchery Salmon

Posted on May 21, 2019 by Tom Cannon

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 (>55^oF) in these drier years (Figure 3), as were Delta temperatures (>68^oF; 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:

Release smolts in the American River in wetter years with higher river flow and lower river water temperature.
Release smolts in the Bay in dry years; do not release in river.
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.

https://www.rmpc.org ↩

Winter Trawl Survey – Delta Smelt 2019 Adult Spawning Run Update

Posted on May 12, 2019 by Tom Cannon

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

Posted on May 10, 2019 by Tom Cannon

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.

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

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 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 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.