Salmon and Sturgeon Compromised in Near-Record Water Year — June 2019

Lower Sacramento River water temperatures exceed water quality standards and lethal levels for newly hatched sturgeon.  In a prior post I discussed compromising water temperatures for sturgeon and salmon under low flows in dry years in the lower Sacramento River (see map, Figure 1).  But I did not expect the Bureau of Reclamation to violate its permit conditions for the Central Valley Project in this record setting wet year.  Flow in the lower river has dropped to 9000 cfs, and water temperature has risen above 20oC (68oF) at Wilkins Slough upstream of the mouth of the Feather River near Grimes (Figure 2; this is downstream of the area shown on the map).  In the week following June 10, Reclamation dropped reservoir release nearly 3000 cfs (Figure 3), leading to the rise in water temperatures.  The water temperature standard of 56oF was also exceeded in the upper river near Red Bluff (Figure 4).  The upper-river standard can be relaxed in drier years, but that would not apply in this near record wet year (Figures 5-8).

Figure 1. Map of the Sacramento River Basin (Princeton Ferry to Keswick Dam)

Figure 2. Water temperature and flow rate of Sacramento River at Wilkins Slough gage near Grimes. Water quality standard for lower river is 20oC (68oF).

Figure 3. Water release from Shasta/Keswick dams in June 2019.

Figure 4. Water temperature of upper Sacramento River near Red Bluff (RDB), Bend (BND), and Balls Ferry (BSF), May-June 2019. Red line is water quality standard for upper river.

Figure 5. Lake Shasta storage in 2019 compared to historical average, wettest, and driest years.

Figure 6. Lake Shasta water level and storage May-June 2019. Lake is at 98% capacity and 118% of average storage on June 15, 2019.

Figure 7. Snowpack in Central Valley December-July. Blue lines are 2019.

Figure 8. Mount Shasta on June 15, 2019.

Poor 2018 Sacramento River Fall Salmon Run Prognosis for 2019 Run

In an October 2018 post, I discussed the record low Sacramento River1 2017 adult fall-run Chinook salmon run and juvenile fall-run production index from winter-spring 2018. Both record lows were indications that something had gone wrong for brood year 2014. I also forecasted a poor adult run in fall 2018. The latest information on salmon runs for 2018, recently published by the California Department of Fish and Wildlife, indicates the 2018 fall run was indeed also poor (Figure 1). The run size in 2018 was 8980 (5th lowest in the record), as compared to 1822 in 2017, and 29,966 in 2014.

Despite a normal water year in winter-spring 2016 in the Sacramento River, the hangover from the critical 2013-2015 water-years drought (low reservoir levels) provided harsh conditions for brood year 2015 fall run that led to the poor adult run in 2018:

  1. Poor river conditions due to low streamflows during the spawning run in summer and late fall 2015 (Figure 2 and 3).
  2. Poor egg-embryo incubation in gravel redds due to low streamflow in late fall 2015 and early winter 2016 (Figure 2).
  3. Poor fry survival from low winter streamflows (February and early March) and poor smolt survival from low late spring streamflows (late April and May) in 2016 (Figure 3).

In addition, most of the 10 million Coleman Hatchery smolts raised for brood year 2015 were released at the hatchery in lower Battle Creek from April 7 to April 29, 2016, under sharply declining streamflows (Figure 3) and rising water temperatures in the lower Sacramento River (Figure 4). Their contribution to the 2018 spawning cohort was similarly low. Of the 10 million smolts released, only 14,000 adults returned to the upper river, as compared with 84,000 in 2012.

Based on the spawner recruit model, the 2018 fall run of 8980 adult salmon could have been three times as high or higher (similar at least to 2012 or 2014) if not for poor river flows and associated high spring water temperatures that exceeded water quality standards.

The prognosis for the upcoming 2019 run is mixed, but the run should show improvement. Early indications are good,2 despite very low numbers of spawners in fall 2016 (red 16 in Figure 1). Water year 2017 was wet (19 will be blue in Figure 1). Coleman Hatchery’s released 10-million smolt to the upper river in April 2017 under optimal conditions. There were stressful warm water (>20oC) and low flow conditions in July-August 2016 early in the 2016 spawning run (Figure 5), as well as low and sharply dropping flows in the fall spawning season that likely caused some redd dewatering and low egg/embryo survival. Maintaining less than stressful water temperature during the early run in summer will be important; conditions are already marginal during late spring when winter-run and spring-run adults are migrating (Figure 6). Flows in the 10,000-14,000 cfs range may be necessary to maintain water temperatures at or below 20oC through the summer. With Shasta Reservoir full and an abundant snowpack, that should be readily achievable.

Hopefully, the 2019 run can approach that of 2012 (green 12 in Figure 1) for that low level of spawners (09 and 16 were similar). The results for summer coastal and river fisheries will be the next indicator of success for the 2019 fall-run salmon.

Figure 1. Spawner-recruit relationship for Sacramento River fall-run in-river estimates of run size (transformed log10-3). The 2018 escapement is shown as large blue dot and associated green “18”. Number indicates spawner estimate for that year (y-axis) as derived from spawners three years earlier (x-axis). Color indicates winter-spring rearing and migration conditions for that brood (winter-spring 2016 for spawners in 2018). Red denotes dry year in first winter-spring. Green denotes normal years. Blue denotes wet years. The 2018 spawner (escapement) number should have been higher, similar to other normal water years. Source: http://calsport.org/fisheriesblog/?p=2333 .

Figure 2. Streamflow in the upper Sacramento River below Shasta/Keswick dams near Redding July 1, 2015 to June 30, 2016. Source: USGS. Note the low late fall and winter streamflows in the primary spawning grounds below Keswick Dam. The decline from 7000 cfs in late October to below 4000 cfs in late December led to significant redd dewatering and poor fry survival. Fall-winter flows should not fall below 5000 cfs.

Figure 3. Streamflow in the lower Sacramento River near Grimes, July 1, 2015 to June 30, 2016. Source: USGS. Note the low summer and fall streamflows in 2015, and low late spring flows in 2016. Poor pre-spawn and spawning season (summer-fall) flows lead to poor adult survival to spawning and poor egg viability. Low spring flows lead to high water temperatures and lower turbidities that increase smolt vulnerability to predation. Flows in the lower river should be maintained above 5000 cfs.

Figure 4. Water temperature in lower Sacramento River at Wilkins Slough in April-May, 2016. Note the Basin Plan water quality standard for lower Sacramento River water temperature requires temperatures no greater than 20oC, 68oF. High water temperatures lead to poor migrating smolt growth and greater vulnerability to predation. Spring water temperatures should not exceed 18oC, 65oF to minimize migrating smolt mortality.

Figure 5. Water temperature and river flow in the lower Sacramento River near Grimes from July 2016 to June 2017. Note that water temperature exceeds 20oC , the stress level for adult salmon and water quality standard, when summer flows fall below about 8000 cfs.

Figure 6. Water temperature and river flow in the lower Sacramento River near Grimes in May 2019. Note that in mid- and late May, water temperature reached near 20oC, the stress level for adult salmon and water quality standard, when flows initially fell to near 8000 cfs.

Selective Chinook Salmon Sport Fisheries in Puget Sound With notes on variants for Coho salmon and Steelhead.

Introduction

The Endangered Species Act (ESA) imposed complex challenges to the management of the sport fishery for Chinook salmon in Puget Sound, Washington State. In order to protect limited stocks of “native or wild” Chinook (i.e., those that are not from hatchery origin and naturally spawn in streams), total closures to sport fishing were strongly considered.

Wild and “hatchery” Chinook (i.e., those that are reared in a hatchery) co-mingle in the same Puget Sound habitat. The hatchery fish are often sufficiently abundant in many areas to allow some level of sport fishing. Total closure of the sport fishery for all Chinook was therefore a major issue for sport fishermen because of the high economic value of the sport, the potential overabundance of adult hatchery fish, and the sport of catching this prized species.

To differentiate hatchery from wild salmon, the adipose fin is removed from hatchery-reared smolts before release. Thus, when an angler brings a Chinook to shore or a boat, the angler can visually determine if it is from hatchery origin, based on the absence of this fin. This allows a mark-selective fishery targeting hatchery fish.

Mark-selective Chinook salmon fisheries are sometimes further constrained by “encounter” quotas. In Puget Sound, quotas for angler “encounters” (a combination of legal-size Chinook, wild Chinook, sublegal hatchery fish, and sublegal wild fish) are established annually for 9 specific marine management areas. For selective river fisheries in the Puget Sound area, the encounter approach is not used.

Current management using quotas on catch and encounters allows sport fisheries on hatchery Chinook salmon. Co-managers Washington Department of Fisheries (WDFW) and Native American Tribes use three major methods to manage the Chinook sport fisheries in Puget Sound:

  1. review of angler punch card data,
  2. creel census surveys supplemented with test boat fishing and aerial surveys, and
  3. quotas on encounters in areas of Puget Sound where sublegal and legal sized Chinook salmon co-mingle.

Punch Cards

In addition to a fishing license, anglers fishing for salmon (all species) and certain other species (e.g., steelhead and halibut) must also purchase a punch card. When one of these species is caught and kept, the angler records the date, location, species, and other information on the card. The punch card must be returned to the WDFW at the end of the recording season. If the cards are not returned, there is a penalty charge made on the next license purchased. The card is used to determine annual harvest and historical trends for the various management areas.

Creel Census

To supplement the punch card information, additional “real time” data are monitored through angler “creel” surveys at various sites. These face-to-face surveys collect information on species caught and kept, number of fish released (including any wild salmon, sublegal fish, others species), hours and management area fished.

Encounters

Recording encounters involves the reporting during creel surveys of all Chinook kept and released, including whether fish caught were legal-sized and adipose clipped, legal-adipose intact, sublegal-adipose clipped, or sublegal-adipose intact. Information collected during the creel surveys also records Chinook retained and an estimate from the angler of those that have been hooked and released (legal, sublegal, or native). This information is supplemented by test boat fishing and aerial surveys.

During the pre-season, each of the 9 management areas in Puget Sound is assigned specific seasonal encounter quota numbers. If any of the quotas are reached in an area, that area is closed to further fishing for Chinook.

Discussion

Mark-selective sport fisheries on hatchery salmon in the Puget Sound have been allowed through the use of quotas on angler catch and encounters for specific management areas. The quotas are determined during the pre-season by the fisheries co-managers WDFW and the Tribes. Quotas are derived from a model that includes historical punch card data, spawning surveys from earlier years, and other population and catch data.

The sport fishery for Chinook has severely declined in recent decades. There is a wide array of potential reasons for this decline. These include massive increases in predators (e.g., seals and sea lions), ocean conditions, loss of freshwater habitat, and others. In past decades, fishing for Chinook salmon was open the entire year, with much higher daily limits (up to 3 fish). The fishery has been severely reduced to only a few weeks in summer and limited months in the winter, often with only a 1 fish daily limit. The addition of the encounters approach in recent years has also contributed to large crowds that are condensed into the shortened periods. This, for some, has catching a prized Chinook salmon a lot less enjoyable.

In general, the encounters approach has been useful for allowing Chinook salmon sport fishing to continue on a limited basis while maintaining protections for wild Chinook. There are some drawbacks, however. For example, if the pre-season estimate of Chinook abundance for a particular management area is underestimated, the encounters quota may be reached early and the season closed, even though there may be substantially high survival rates that might have allowed a higher quota value.

Coho salmon and steelhead are also adipose clipped at the hatchery. This allows selective sport fisheries for these species to continue as well, while allowing release of wild spawning adults. However, the encounters methodology is not currently used for these species (capture of sublegal fish is low). In areas where adult Coho populations are low, a selective fishery may occur, in which only hatchery fish are allowed to be retained. However, in areas where populations of “native” Coho are abundant, both wild and hatchery Coho may be kept.

In general, nearly all steelhead management areas in Washington require release of native steelhead, which, in most cases, have a high survival rate when released.

In sum, these mark-selective sport fisheries in Puget Sound allow sport fisheries that otherwise might be banned altogether. Harvest of hatchery fish may also help reduce competition with wild fish for spawning habitat and food resources.

 

Wet Winter-Spring 2019 Good for Central Valley Salmon

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?

  1. January-February flow pulses that carry fry to Bay-Delta rearing habitats.
  2. 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 (<20oC, 68oF) 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 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 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 20oC.

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 20oC.

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 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.

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

 

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

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.

  1. 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.
  2. 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 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 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 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 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 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 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 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.

Figure 8. Delta outflow in spring 2014.