Increasing Salmon Rearing Habitats in the Upper Sacramento River – A Long-Overdue Management Action

Large amounts of rearing habitats for young salmon were lost in the upper Sacramento Valley Basin when Shasta and Keswick Dams were built. Loss of this rearing habitat (located in smaller, shallower river channels upstream of the dams – like the McCloud River) was considered one of the numerous reasons for the listing of the winter-run Chinook as endangered. Since dam construction, young salmon emerging from main-stem spawning areas downstream of the dams must now contend with the severe rigors of a large, deep river channel. It is generally acknowledged that the quality of rearing habitats in those upstream areas was superior to habitats below the dams (Vogel 2011).

Although significant efforts have been made to increase the quantity and quality of spawning habitats below the dams, minimal progress has occurred on rearing habitats. Massive amounts of spawning gravels have been added to the upper Sacramento River downstream of Keswick Dam, but there are indications that rearing habitats may be an equally important, if not more-important, factor limiting the fish populations. As pointed out by the U.S. Fish and Wildlife Service (USFWS),“ … there would be little value in increasing the quantity of available spawning gravel if the problem that actually limits juvenile production is lack of adequate rearing habitat” (USFWS 1995). Astonishingly, more than two decades later and despite over 1 billion dollars spent on salmon restoration, that potential dilemma remains unresolved.

Present-day rearing habitats are considered very limited and predation during juvenile rearing is believed to be a stressor of very high importance (NMFS 2014). The best habitats, in conventional theory, would be on the channel fringes. Indeed, some such areas with desirable attributes do exist, but are sparse. However, due to the nature of the river reach where most winter-run salmon spawn in deep water, many of the ideal habitat characteristics for rearing are lacking (e.g., appropriate velocities and cover). Subsurface structures like woody debris are severely deficient and would be challenging to restore due to lack of significant recruitment and periodic extremely high-flow events (Shasta Reservoir flood-control releases) that would dislodge this essential feature. In many areas where salmon spawn, the river is wide (e.g., 500 feet) and channel edges are deep (Figure 1). Fry emerging from redds in the main-stem riverbed encounter a paucity of velocity and predator refugia. Underwater observations and sonar camera footage near artificial structures in deep water (e.g., bridge piers) have frequently shown extensive salmon rearing activity, but may suggest the fish are utilizing those areas because insufficient other natural structures on the riverbed are limited or absent (Vogel 2011).

Figure 1. Cross-sectional profile of the upper Sacramento River in an area 500 feet wide and 10 feet deep (scale is approximate).

Figure 1. Cross-sectional profile of the upper Sacramento River in an area 500 feet wide and 10 feet deep (scale is approximate).

Based on many years of observations in the main-stem Sacramento River, large schools of young salmon exhibit a very strong affinity for specific habitats unique in a large, deep river channel. This circumstance is a quandary for salmon fry upon emergence from redds positioned in deep water and long distances from channel edges. The weak-swimming fry are immediately exposed to high near-bed water velocities and minimal refugia to escape from predatory fish such as rainbow trout that are very abundant in areas where winter-run Chinook spawn. The region where young salmon have been observed in deep channel areas include behind tail spills of redds and bridge piers, and in eddies adjacent to vertical bedrock walls. It is particularly evident that large schools of salmon choose areas where eddies exist adjacent to high water velocity shear zones. This provides the fish necessary velocity refugia while simultaneously gaining ready access to drift food organisms, thereby minimizing energy expenditure. Unfortunately, those same areas do not provide refuge from predatory fish.

The following are examples of salmon rearing in the deeper waters of the upper Sacramento River. [It must be noted that an enormous amount of sonar camera footage (not shown here) has been taken along near-shore shallow areas that did not show significant rearing utilization.] After viewing each video, stop or click “cancel” on the YouTube player to allow viewing of subsequent videos in this blog entry. For the sonar camera footage, juvenile Chinook can be discerned by largely maintaining their positions in the current, exhibiting visible swimming movements. Ensonified objects moving with the current are debris drifting downstream (e.g., algae and weed fragments).

  • A school of winter-run Chinook fry rearing on the riverbed adjacent to an Interstate-5 bridge pier and woody debris in the Sacramento River at water depths of 10 feet:
  • School of juvenile Chinook salmon rearing behind a Lake Redding bridge pier in the Sacramento River at water depths approximately 10 feet deep:
  • School of juvenile Chinook salmon rearing in the Sacramento River in very deep water alongside a vertical bedrock wall and behind woody debris and filamentous algae or weeds:
  • School of juvenile Chinook salmon rearing in the Sacramento River behind the remnants of a concrete bridge pier on the riverbed in water depths approximately 12 feet deep with a large fish swimming through the school:

An action identified in the 2014 National Marine Fisheries Service (NMFS) Salmon Recovery Plan is: “Using an adaptive management approach and pilot studies, determine if instream habitat for juvenile salmon is limiting salmonid populations, by placing juvenile rearing-enhancement structures in the Sacramento River.” Evaluation of such measures is also a priority in the USFWS Anadromous Fish Restoration Program (USFWS 2001). Most recently, NMFS (2016) identified “a lack of suitable rearing habitat in the Sacramento River” as an “important threat” to winter-run Chinook. Therefore, a proposal to place rearing habitat structures in some deeper-water areas (approximately > 8 feet) of the main-stem upper Sacramento River was recently developed. Using guidance from the California Department of Fish and Wildlife’s (CDFW) Stream Habitat Restoration Manual (CDFW 2010), woody debris heavily anchored to the riverbed using large, angular boulders has been recommended for this initial step and has received favorable response from the fishery resource agencies. Angular boulders would provide the dual benefits of firmly securing woody debris and providing velocity refugia for young salmon; woody debris would provide predator refugia.

It is important to emphasize that this proposal is a pilot project and not intended to create nearshore, shallow-water habitat attributes similar to those that existed in upstream areas prior to dam construction or were lost in downstream riparian areas afterwards. There are already separate plans to construct small, shallow-water side channels in the main-stem river to address that issue. In contrast, this project is intended to place structures in completely different rearing habitat zones in deeper water where large numbers of young salmon have been observed. Given the ecological realities of the specific and unique environmental conditions in the upper Sacramento River, deep-water rearing habitats could very well be one of the most important environmental variables affecting the survival of main-stem spawning salmon progeny. If the pilot project determines high rearing utilization, the project could easily be expanded.

Sites chosen for rearing habitat placement should be in the vicinity and downstream of known spawning sites that are currently lack good rearing habitats. To provide the most benefit to young salmon, placement of rearing structures is focused on the approximate 12-mile reach of the upper Sacramento River below Keswick Dam. This area is where nearly all the endangered winter-run Chinook have been spawning in recent years and also supports the other three Chinook runs as well as the threatened steelhead.

Hopefully, a pilot project will be implemented in early 2017 … stay tuned.

Literature Cited

California Department of Fish and Wildlife. 2010. California Salmonid Stream Habitat Restoration Manual. July 2010.

National Marine Fisheries Service. 2014. Recovery plan for the Evolutionarily Significant Units of Sacramento River winter-run Chinook salmon and Central Valley spring-run Chinook salmon and the Distinct Population Segment of California Central Valley steelhead. California Central Valley Area Office. July 2014. 406 p. /domains/california_central_valley/final_recovery_plan_07-11-2014.pdf

NMFS. 2016. Species in the Spotlight. Priority Actions: 2016 – 2020. Sacramento River Winter-Run Chinook Salmon, Oncorhynchus tshawytscha. 16 p. _salmon_spotlight_species_5_year_action_plan_final_web.pdf

U.S. Fish and Wildlife Service. 1995. Working paper: habitat restoration actions to double natural production of anadromous fish in the Central Valley of California. Volume 1. May 9, 1995. Prepared for the U.S. Fish and Wildlife Service under the direction of the Anadromous Fish Restoration Program Core Group. Stockton, CA.

U.S. Fish and Wildlife Service. 2001. Final Restoration Plan for the Anadromous Fish Restoration Program. A plan to increase natural production of anadromous fish in the Central Valley of California. Released as a revised draft on May 30, 1997 and adopted as final on January 9, 2001. 106 p. plus appendices.

Vogel, D.A. 2011. Insights into the problems, progress, and potential solutions for Sacramento River basin native anadromous fish restoration. Report prepared for the Northern California Water Association and Sacramento Valley Water Users. Natural Resource Scientists, Inc. April 2011. 154 p.

Central Valley Salmon Require Improved Resilience

A suite of disturbances in the Central Valley has eroded many of the inherent characteristics that once conferred resilience1 in historically abundant salmon populations.  Resilience is provided by natural abundance, diverse run timing, multiple habitats, and broad habitat availability and connectivity.  Last November, I recommended a dozen specific actions to save winter-run salmon.  This post focuses on long-term actions to restore resilience in Central Valley salmon populations and fisheries.

Resilience has declined due to the narrowing of optimal adult migration conditions, the confinement of spawning to localized areas and time periods, the limitation of outmigration periods and regional conditions, the confinement of rearing periods, and the amount of and connectivity of geographical habitats.

Confinement of salmon below dams constructed in the 1940’s  took away much of the resilience in the salmon populations.  In the past 70 years, the populations have depended upon a narrowing range of habitat conditions in time and space in the limited spawning habitat below Shasta and other major rim dams, as well as in the migration and rearing habitat between these spawning areas and San Francisco Bay.  The development of the State Water Project further diminished Central Valley salmon’s remaining resilience.

Resilience has been lost in following ways:

  1. Spawning habitat has gradually declined below dams due to lack of new gravel recruitment and the gradual armoring of spawning riffles.
  2. Spawning habitat has declined with weakened management of water temperature below Shasta, narrowing the spawning reach from 40 miles to as little as 10 miles. Early spawning of winter-run salmon in April and May has been lost even in wetter years like 2016 because of flow reductions in these months and because the temperature of water released from Shasta in these months has been increased.
  3. Embryo survival in redds and fry survival in rearing reaches has been compromised by low, warm summer and fall flows. More redds are dewatered with more frequency as water deliveries for irrigation taper off in the fall.
  4. Winter flows that carry juveniles to and through the Delta are lower and more sporadic. Fall and early winter flows and pulses that occurred historically and enhance smolt emigration no longer occur to the extent they once did, particularly in the spawning reaches immediately below the major reservoirs that regulate all the inflow.
  5. With lower and warmer river and Delta flows, salmon predators have become increasingly more effective.
  6. The quality of the physical habitat of salmon, and winter-run salmon in particular, has been adversely modified over time.

Hatcheries can reduce resilience over time if specific precautions are not taken to avoid weakening the gene pool and population diversity, and to avoid interactions with wild fish.  But hatcheries can also be used to strengthen resilience by increasing genetic diversity and spreading populations in time and geographical range.

Habitat restoration can increase resilience by limiting bottlenecks such as lack of spawning gravels or migration corridor connectivity.  Flow and water temperature remain the two most important habitat factors in the Central Valley.  The availability of floodplain rearing habitat is also important.  Reduced winter flooding resulting from global warming and lower reservoir carryover storage levels has reduced habitat resilience over time.  The gradual decline of large wood in Valley rivers over the decades has reduced the rearing capacity of streams and rivers.  River and stream channels have gradually degraded due to scour and the lack of large wood and natural sediment supplies.

A resilience-based approach is likely to be more successful than traditional mitigation or restoration approaches “by seeking to rebuild suites of disturbance-resistant characteristics” that were historically present in the Central Valley.  A resilience-based strategy “emphasizes the diversification of life history portfolios” and “would seek to maintain a diversity of habitat types, including less productive habitats that may have primary importance only as refugia or alternate spawning habitat during disturbances.”  The ultimate goal is to get salmon smolts to San Francisco Bay and the ocean, which offer cold waters and abundant food.

Historically, resilience occurred at all life stages, beginning with an abundance of adults.  With the present depressed adult runs, resilience is thus already handicapped.  Building runs requires restoring resilience of all life stages, starting with egg survival.  Turning around the decades of decline in resilience and increasing it, especially in the short term to avoid extinctions, is a therefore a major, expensive undertaking.  First, we should focus on stopping further declines in resilience.  Second, we should improve resilience where we can to begin the healing.  The following are some suggestions:

  1. Increase the salmon spawning reach below Shasta in time and space by providing better flows and water temperatures. Extend the spawning reach back down to Red Bluff and diversify timing with better early season conditions (e.g., April-May winter run spawning).  Improve physical habitat further downstream toward Red Bluff, not just near Redding.  Extend habitat improvements where possible into tributaries (e.g., Clear and Battle Creeks).
  2. Extend the range of salmon into former habitats, such as the planned improvements on Clear and Battle creeks, and in the reaches above selected rim dams.
  3. Expand the conservation hatchery program to diversify genetics and support expanded range. Select for specific natural genetic traits that have been lost or changed to increase diversity.
  4. Develop and implement a river flow management plan for the Sacramento River downstream of Shasta and Keswick dams that considers the effects of climate change and balances beneficial uses with the flow and water temperature.
  5. Increase the range in time and space of rearing and migratory habitats that accommodate diversity.
  6. Develop and implement a long-term large wood and gravel augmentation2 plan consistent with existing plans and flood management to increase and maintain spawning habitat for salmon and steelhead downstream of dams. Diversify habitats and reduce habitat bottlenecks.  Expand rare and important habitat types.
  7. Counteract where possible the effects of climate change. Where changes in flow and water temperature changes delay smolting, make changes that return diversity.
  8. Provide a more natural diversity of flow pulses immediately below major dams during the emigration season (i.e., December-April) to diversify the timing and life stages of the emigration of juvenile salmon.

A final note:

Instead of improving resilience, the Delta “WaterFix” will only cut further into and adversely modify the resilience of the salmon populations.  There will be more demands on Shasta storage to meet new Tunnel diversion capacity.  Flows below the Tunnel intakes will be lower, further reducing resilience by warming through-Delta spring migration routes (Figure 1).  Less freshwater flow into the Delta will further alter Delta habitats and make them more conducive to non-native invasive species of plants and animals.  Delta habitat will be warmer earlier in the season, less turbid, and more brackish.

Figure 1. Water temperature versus mean daily flow at Rio Vista in spring 2016. (Source of data: CDEC). Resilience in terms of Delta migration survival would be reduced by the effects of the proposed WaterFix on water temperature in the Delta spring migration route.

Figure 1. Water temperature versus mean daily flow at Rio Vista in spring 2016. (Source of data: CDEC). Resilience in terms of Delta migration survival would be reduced by the effects of the proposed WaterFix on water temperature in the Delta spring migration route.

  1. Resilience Approach or Portfolio Effect – The “portfolio effect,” is the coexistence of multiple life history strategies within a population – how diversity in life history can increase resilience and stability.

Questions for Bay-Delta Science

The Interagency Ecological Program (IEP) for the Bay-Delta is about to hold its annual workshop on their science program and their plans for 20161.  Science is based on hypotheses and hypothesis testing – or in other words, addressing questions.  Here are some questions that would be appropriate for the Bay-Delta Science team to address, if it is not already addressing them:

  1. Montezuma Slough is the critical waterway connecting Suisun Marsh with Suisun Bay. It begins near the confluence of the Delta outlets of the Sacramento River and San Joaquin River near Collinsville.  It ends at its outlet in west Suisun Bay near the Mothball Fleet.  It is about 16 miles long, with strong tidal flows and salinity gradients.  The salinity control structure (gates) installed in 1988 at the upper end opens on an ebb tide to let freshwater from the Sacramento River downstream into the Slough and Suisun Marsh, and closes on the flood tide to keep saltier water from entering at the bottom to replace the fresher water.  The Slough has always been an important nursery for Bay-Delta fish including longfin and Delta smelt, as well as striped bass.  In wet years it is fresh much of the year, while in drier years it is brackish.  Questions:  How has the Slough’s role changed as a nursery area, especially in spring and summer, with changes in the Bay-Delta water quality standards after 1994, with operation off the Salinity Control Structure, with implementation of biological opinions in 2008-09, and with changes related to the Temporary Urgency Change Petitions during the 2012-2015 drought?  Have changes in and to the Slough contributed to the possible extinction of the smelts and reductions in estuary productivity?
  2. Cache Slough is a backwater tributary of the lower Sacramento River channel in the northern Delta. It is the outlet of the Yolo Bypass and the outlet entrance of the Deep Water Ship Channel and Port of Sacramento. It changed permanently with the breaching of adjacent Liberty Island in the late 90’s.  In the past, it received freshwater inflow from the Port, but the Ship Channel gates were closed permanently several decades ago.  The North Bay Aqueduct diverts freshwater from the west end of the slough complex.  The Cache Slough Complex plays an important role in the north Delta ecosystem with its freshwater inputs, shallow water habitats, and large tidal exchange.  In wet years, it receives large flood flows of the Yolo Bypass of the Sacramento River.  It is an important spawning and nursery area of both smelts and splittail, and is an important nursery of salmon in winter-spring of both dry and wet years.  Many very deep holes in the complex are known habitat areas of adult and juvenile sturgeon.  The deep water of the Ship Channel appears to support a significant portion of the Delta smelt population.  The Complex has more productivity and food than the adjacent Sacramento River channel.  The Complex is thought to contribute significant nutrients and organic carbon sources to the northern Delta.  Questions:  Are plankton blooms in the Complex a function of shallow tidewaters with long residence times or high nutrients or both?  Has the role and ecology of the Complex changed over the past several decades with changes in Liberty Island, operation of the Yolo Bypass, operation of the North Bay Aqueduct and Ship Channel, and changes to Delta standards (including recent TUCP’s)?  Would proposed drought year barriers on Miners and Steamboat sloughs cause additional changes to lower Cache Slough?  Would added streamflow through the Bypass and Ship Channel provide benefits to the ecology and fisheries dependent on Cache Slough and the northern Delta?  Would more flow through the Bypass improve habitat and habitat use by young salmon moving upstream from the lower Sacramento River channel?  Is there more smelt spawning in the Complex in drought years because of salt intrusion into western Delta?  Can the isolated population element of Delta Smelt in the Complex survive the warm summer conditions?  Would the Complex benefit from more tidal marsh and supratidal floodplain?  Does the Complex benefit from nutrient inputs of local and regional treatment plants and agricultural drainage?  Do water supply diversions by agriculture and the North Bay Aqueduct affect habitat benefits to the Complex and the Delta?
  3. The Delta Cross Channel (DCC) that connects the lower Sacramento River channel in the north Delta with the San Joaquin River channel in the central Delta via the forks of the Mokelumne River can be opened or closed to control the amount of Sacramento channel water that reaches the central and south Delta. Closing the DCC forces more water and juvenile salmon down Georgiana Slough.  Questions:  Would opening the DCC in spring benefit smelt and salmon?  In particular, would salmon outmigrating from the San Joaquin River benefit?  Would Sacramento salmon that pass into central Delta via Georgiana Slough benefit from open DCC?
  4. The Head of Old River Barrier (HORB) reduces the flow of the San Joaquin River into the head of Old River near Stockton. HORB keeps most juvenile salmon that are moving down the San Joaquin channel out of Old River water that is drawn to South Delta export pumps.  However, while HORB keeps San Joaquin salmon moving toward the central Delta, the reduction of San Joaquin flow into the head or Old River increases flow toward the pumps from the central Delta (increasing negative OMR flows up to 1000 cfs).  Questions:  Would HORB function improve with installation of False River Barrier and opening of the DCC?  How would the tradeoff in export potential balance with benefits to San Joaquin salmon?
  5. The False River Barrier blocks tidal flows from the lower San Joaquin River channel at Jersey Point into Franks Tract in the Central Delta. This reduces flow of brackish water and nursery habitat of smelt into the central and south Delta in dry years.  Questions:  Would placement of the False River Barrier in spring of wet years provide benefits to smelt and Delta habitats of smelt and reduce entrainment of smelt into the south Delta?
  6. Summer Delta Outflow and Exports are unrestricted except for salinity standards based on agricultural use. Summer exports from South Delta are generally maximized unless they are restricted by high salinities in drought years (low reservoir releases during droughts).  Questions:  Would higher summer outflows that keep the LSZ west of the Delta during periods of high export protect smelt and LSZ habitat?  Should summer salinity standards be changed to protect LSZ from moving east into the central Delta?  Would higher Delta outflow in summer be beneficial to Bay nursery of many estuary and marine fish including herring and anchovy?  Would higher summer outflow improve productivity of the LSZ?
  7. Conditions for salmon rearing in the Delta during the Winter can likely be improved. Nearly all the salmon runs in the Central Valley spend part of their first year rearing in the Delta in the winter and migrating through the Delta to the Bay and ocean.  Winter Run and Late Fall Run hatchery and wild smolts come through in December-January with the first flow pulses from the upper Sacramento River.  Spring and Fall Run fry, parr, and smolts come through from January to March or even into April.  The fry and parr depend on the Delta and upper Bay, rearing there during the winter before smolting.  Questions: How can migration period flows be optimized to improve survival?  Can optimal rearing habitats be identified and improved?  How can Delta inflows from the San Joaquin River be improved during winter to enhance San Joaquin salmon survival?
  8. Delta Water quality standards are monthly, biweekly, or weekly. Questions:  What are the upsides and downsides of moving to more frequent real-time management of Delta water quality standards, as well as management of fish and fish habitat?  Have existing requirements to change operations “when fish are present” been effective?  What are the ecosystem effects of shortening the time-step for management decisions and relying on short term response for changes in operations?  What structural measures would allow managing agencies to better maintain their independence from conflicting pressures? 
  9. Smelt growth and survival could be enhanced by improving pelagic habitats within and downstream of spawning areas. Water temperature, turbidity, and zooplankton production/biomass/concentrations are key factors in growth and survival.  Question: Can Bay-Delta habitats be managed on a real-time basis to optimize smelt growth and survival?
  10. Green and White Sturgeon spawning as well as egg, larvae, and juvenile survival are dependent on flows and water temperatures in the Sacramento River between Red Bluff and the Delta. Question:  How can the middle reaches of the Sacramento River be better managed to improve sturgeon survival?
  11. Cache Slough/Yolo Bypass salmon and sturgeon adult migrations are attracted by strong tidal exchange, but those attracted may stray into Bypass tributaries (Putah and Cache Creeks) or the Colusa Basin Drain, or become stranded below Fremont Weir at the northern end of the Bypass. Young salmon enter the Bypass during Fremont Weir spills under high river flows.  Questions:  How can migration conditions be enhanced without increased straying and stranding in the Bypass?  How can the Bypass become a beneficial corridor for adult sturgeon and salmonids targeting upper Sacramento River spawning grounds?  How can more flow and young salmon be routed through the Bypass to improve growth and survival of the overall populations?
  12. San Joaquin salmon and steelhead migrations through Delta are disrupted by the nearly total loss of San Joaquin River water to exports in drier years. Questions:  Does placement of the Head of Old River Barrier enhance the signature of the River reaching the Bay?  Would enhanced San Joaquin River flow and reduced exports at key times of the year benefit migrating San Joaquin River salmon and steelhead?
  13. Delta primary and secondary productivity has declined over the past several decades. Questions:  Do exports remove nutrients, planktonic habitat, or adversely disrupt the Low Salinity Zone by entraining pelagic habitat from the west and central Delta via Dutch Slough, Threemile Slough, False River, and the mouth of Old River?  Is the replacement of an entrained LSZ and freshwater pelagic habitat by unproductive, warmer reservoir water detrimental to Delta pelagic habitat productivity?  Has the invasion of rooted and floating aquatic plants reduced pelagic habitat productivity?  Is the invasion of non-native plants related to shorter residence time and continued replacement of entrained pelagic habitat and replacement of reservoir water?  Has the invasion of aquatic plants been aided by reduced phytoplankton productivity and influx of low turbidity reservoir water?
  14. Dutch Slough and other Central Delta habitat restoration projects would expand intertidal and subtidal habitats. Questions: Would such projects expand habitats of non-native fish and aquatic plants? Would the new pelagic habitats be subject to entrainment by south Delta exports?
  15. Survival of salmon and steelhead juveniles in the Delta and lower rivers upstream of the Delta is poor because of degraded habitat, poor flows, poor water quality, and predators. Questions:  Would barging hatchery and wild salmon to the Bay particularly in drier years when flows are low improve survival and minimize straying? Would out-planting wild and hatchery salmon to more optimal Bay-Delta floodplain rearing habitats improve overall production?

Winter Run Salmon – “Species in the Spotlight”

Winter Run

Species in the Spotlight

The National Marine Fisheries Service (NMFS) has included the Sacramento River Winter-Run Chinook Salmon in its “Species in the Spotlight,”1 one of the eight species under NMFS’s jurisdiction nationwide that are most at risk of extinction.

On its website, NMFS describes the condition of Winter-Run (in italics below):

State and Federal Agencies, public organizations, non-profit groups and others in California’s Central Valley have formed strong partnerships to save Sacramento River winter-run Chinook salmon. Efforts to protect winter-run Chinook salmon include restoring habitat, utilizing conservation hatchery programs, closely monitoring the population, and carefully managing scarce cold water. Additional key actions needed to safe guard winter-run Chinook salmon from further declines include:

  • Improving management of Shasta Reservoir’s storage in order to provide cold water for spawning adults, eggs, and fry, stable summer flows to avoid de-watering redds, and winter/spring pulse flows to improve smolt survival through the Delta. (Note: badly needed as these actions have been generally lacking especially in the past two years.)
  • Completing the Battle Creek Salmon and Steelhead Restoration Project and reintroducing winter-run Chinook salmon to the restored habitat. (Note: Badly needed with little progress made in regard to Winter Run.)
  • Reintroducing winter-run Chinook salmon into the McCloud River. (Note: Badly needed with little progress made.)
  • Improving Yolo Bypass fish habitat and passage so juveniles can more frequently utilize the bypass for rearing and adults can freely pass from the bypass back to the Sacramento River. (Note: Badly needed with little progress made.)
  • Managing winter and early spring Delta conditions for improved juvenile survival. (Note: During the past four years of drought, Delta outflow has almost always been inadequate for emigrating juveniles.)
  • Conducting landscape-scale restoration throughout the Delta to improve the ecosystem’s health and support native species. (Note: Little progress has been made.)
  • Expanding LSNFH facilities to support both the captive broodstock and conservation hatchery programs; (Note: In progress. The hatchery program released 600,000 smolts in February last year and 400,000 in February this year. The releases are made in Redding where flows have been too low for good survival because Shasta Reservoir is retaining all its inflow. Much greater survival would be achieved if the smolts were trucked downstream to mid-river and then barged to the Bay.)
  • Evaluating alternative control rules used to limit incidental take of winter-run Chinook salmon in ocean fisheries. (Note: Ongoing and in progress. Fishery harvest for all races of Chinook will likely be curtailed this year.)

Number One Threat

The most serious threat to Winter Run and the major cause of the nearly complete loss of the past two years’ production relates to the first item in the above list: improving management of Shasta Reservoir cold water storage is essential. The change from a 58°F daily-average water temperature standard at Redding (last summer) to 53°F as proposed by NMFS will greatly help by alleviating sporadic lethal conditions that occurred last summer (Figures 1 and 2).

Achieving non-lethal conditions through the summer is possible by conserving Shasta Reservoir’s cold-water pool, which is best achieved by reducing inputs of warm water from Whiskeytown Reservoir (from Lewiston-Trinity reservoirs) into Keswick Reservoir via the Spring Creek Powerhouse (Figure 3). This source of warm water made up about 15% of the release to the Sacramento River from Keswick Reservoir, and required use of extra Shasta’s cold-water pool water to meet the relaxed temperature standard of 58°F in the upper Sacramento River below Keswick in Redding.

Another source of warm water to Keswick Reservoir was from daily afternoon peak power releases from Shasta Dam (Figure 4). High releases in afternoons raised water temperatures in Keswick Reservoir, requiring more cold-water pool release to compensate for warm water inputs. Apparently, the operations were too complicated for Reclamation to maintain the required 58°F average daily temperature at the mouth of Clear Creek (CCR gage: Figure 1). Operations at other times (e.g., first week in August) indicate clearly that Reclamation had the capability of keeping the water temperature well below lethal levels.

Figure 1. Lethal water temperature extremes for salmon eggs and fry (red circles) near Redding in summer 2015. Green circles denote non-lethal conditions that can be maintained with proper management of Shasta’s cold-water pool.

Figure 1. Lethal water temperature extremes for salmon eggs and fry (red circles) near Redding in summer 2015. Green circles denote non-lethal conditions that can be maintained with proper management of Shasta’s cold-water pool.

Figure 2. Episodes of high water temperature in Keswick Reservoir (red circles) in summer 2015. Peaks were due to hydropower peaking and specific operations of the Shasta Temperature Control Intake Tower to powerhouses at Shasta Dam.

Figure 2. Episodes of high water temperature in Keswick Reservoir (red circles) in summer 2015. Peaks were due to hydropower peaking and specific operations of the Shasta Temperature Control Intake Tower to powerhouses at Shasta Dam.

Figure 3. Warm water (red circle) entering Keswick Reservoir from Whiskeytown Reservoir via Spring Creek Powerhouse in summer 2015. Daily range of 1°F is due to hydropeaking operations.

Figure 3. Warm water (red circle) entering Keswick Reservoir from Whiskeytown Reservoir via Spring Creek Powerhouse in summer 2015. Daily range of 1°F is due to hydropeaking operations.

Figure 4. Warm water releases (red circle) from Shasta Reservoir during daily hydropeaking operations in summer 2015. Release water temperatures in the first week of August and September were lower because of lower afternoon hydropower peaking releases of warm water along with more night-morning cold water pool releases.

Figure 4. Warm water releases (red circle) from Shasta Reservoir during daily hydropeaking operations in summer 2015. Release water temperatures in the first week of August and September were lower because of lower afternoon hydropower peaking releases of warm water along with more night-morning cold water pool releases.


Largemouth Bass Production in the Delta

I had the unique opportunity to study fish use of shallow inshore waters of the western Delta in 1978-79 and again in 2004-05. One of the biggest differences I noticed after 25 years was the increase in Largemouth Bass production. Mitigation areas where levees were breached allowing tides to enter-and-leave tidal ponds without flow-through were virtual Largemouth breeding factories. Areas where channel entrances had filled in and circulation reduced also were prone to aquatic plant proliferation and an abundance of non-native lake/pond fish including Largemouth, sunfish, and shiner minnows. Flow-through areas and tidal channels with two ends had lower Largemouth production (and more native fishes). Limited tidal circulation also caused prolific amounts of aquatic vegetation including water hyacinth, Egeria, milfoil, Parrots Feather, and Potamogeton. Dense beds of aquatic vegetation also occurred in bays, dead-end sloughs, breached islands, and protected shorelines.

A recent study1 relates higher Largemouth production to increases in aquatic plants, specifically relating the abundance of young Largemouth to Egeria. They also found young Largemouth more abundant in warmer waters, another feature of backwater areas. Aquatic plants slow currents, capture sediment, and absorb sunlight, which all contribute to warming of shallow waters.

One of the paper’s conclusions related to future habitat restoration:

“While these efforts will expand the largely missing shallow-water habitat in the Delta, a major concern is that increased shallow water area will expand the habitat for Brazilian waterweed and consequently increase the abundance of Largemouth Bass, creating a predation sink for target native fishes (Brown 2003).”

I have some points of disagreement with these conclusions. First, I do not believe the Delta lacks shallow water habitat. The problem, rather, is that too much of existing shallow water habitat is bad habitat more conducive to non-native warm water fish. Second, good shallow habitat along the edges of the bays and rivers has been and continues being lost to riprapping, ship-channel dredging, remnant soft-levee erosion, and filling with sediment.

I concur with the paper that much planned restoration will create more bad habitat. Instead we should be protecting good habitat and converting more of the bad habitat to good habitat.

For more on the subject of Delta habitat restoration see: .