Shasta River Fall Run Chinook Salmon – Status and Future

In an April 10, 2017 post, I described a sharp decline in the Klamath River salmon runs after the 2012-2015 drought. In that post, I also noted the high relative contribution of the Shasta River run to the overall Klamath run, especially in the past six years. The recent upturn in the Shasta River run and its greater contribution to the overall Klamath run is likely a consequence of efforts by the Nature Conservancy and others to restore the Big Springs Complex of the upper river near Weed, Ca.

The Shasta run has increased measurably since 2010 (Figure 1). Cattle were excluded from Big Springs Creek in 2009, and flows, water temperature and juvenile Chinook densities were markedly improved in and below Big Springs Creek.1 The improved juvenile salmon production likely contributed to greater runs from 2011-2015 and to a higher than expected 2016 run given the 2013-2014 drought (Figure 2). The improvement in the Shasta run bodes well for the Shasta and Klamath runs (Figures 3 and 4). The Shasta run recovery is key to sustaining and restoring the Klamath run and coastal Oregon and California fisheries that depend on the Klamath’s contribution. The Shasta River’s spring-fed water supply comes from the Mt. Shasta volcanic complex. This water supply is resilient to drought and climate-change. The reliability of the Shasta River’s water supply makes the Shasta River’s contribution to Klamath salmon runs particularly important.

Restoration of the Shasta River and recovery of its salmon and steelhead populations has only just begun. Further improvements to the Big Springs Complex, especially to its spring-fed water supply (Figure 5) and to its spawning and rearing habitat, are planned. There is also much potential to improve habitat above the outlet of Big Springs Creek, both in the Shasta River and Parks Creek. There is further potential for habitat restoration in downstream tributaries (e.g., Yreka Creek and Little Shasta River). Reconnection of the upper Shasta River above Dwinnell Reservoir to the lower river would restore many miles of historic salmon and steelhead producing habitat.2 These improvements could make it is possible for the Shasta River to once again produce over half the “wild” (non-hatchery) salmon of the Klamath River.

Figure 1. Fall-run Chinook salmon escapement (spawning run) estimates for the Shasta River from 1978 to 2016. Data Source: CDFW GrandTab.

Figure 2. Mean annual Shasta River streamflow (cfs) as measured at Yreka, CA. Source: USGS. Designated water-year types in this figure are the author’s estimates.

Figure 3. 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 2011-2016, even though the latter period included the 2012-2015 drought.

Figure 4. Estimates of fall-run Chinook salmon escapement for the Klamath River, 1978-2016. Data Source: CDFW GrandTab.

Figure 5. Examples of Shasta River monthly average flows as measured at the lower end of Shasta Valley. Streamflow is low from late spring through summer because of surface and groundwater irrigation demands. October flows are higher because the irrigation season (and season of diversion under some water rights) ends on September 30. Data source: USGS Yreka gage.

Restoring Side Channels in the Upper Sacramento River

In a prior blog entry on this site, the importance of restoring juvenile salmon rearing habitats in the upper main stem Sacramento River downstream of Keswick Dam was described:   http://calsport.org/fisheriesblog/?s=rearing+habitat.  The main river channel is actually a harsh environment for young salmon upon emergence from the river gravels after hatching.  The weak-swimming fry are immediately exposed to very high water velocities and most of the riverbed lacks structure to provide those fish with velocity and predator refugia.  One hypothesis, albeit very difficult to prove, is that insufficient rearing habitats in the upper river may be a significant limiting factor for the salmon runs, particularly for the endangered winter-run Chinook.

Although the notion of increasing the quantity and quality of rearing habitats in the main stem Sacramento River has been discussed for decades, meaningful on-the-ground restoration actions have been lacking.  That circumstance is changing.  A management action now being pursued is the restoration of side channels that have lost ecological functions for salmon rearing, primarily because of diminished or total lack of hydraulic connectivity with the main river channel.   Many of the historical side channels have become plugged, stagnant, and choked with overgrown vegetation; excellent frog habitat, but not for salmon.

A major endeavor to reopen some side channels, probably the most complex in modern times, was recently completed on the upper Sacramento River in Redding, California (Figure 1).  Termed the North Cypress Street Project, multiple agencies and stakeholders successfully planned, initiated, and completed this action in 2016.  Finishing touches on the project were completed just prior to the new year.  Funding was provided by the Central Valley Project Improvement Act Anadromous Fish Restoration Program.  According to the Western Shasta Resource Conservation District which provided oversight for the entire effort, restoration of these side channels will provide rearing habitats for winter-run and fall/late-fall-run Chinook (Figure 2) through the provision of optimal flows, refuge from predators, and increased food sources.  The habitats will be particularly important for winter-run Chinook because nearly the entire population now spawns upstream of the site.

Figure 1.  Location of the North Cypress Street side-channel project to restore juvenile salmon rearing habitats.  The Painter’s Riffle project is located just upstream of Cypress Street which was previously described in this blog:  http://calsport.org/fisheriesblog/?s=painter.

Figure 1. Location of the North Cypress Street side-channel project to restore juvenile salmon rearing habitats. The Painter’s Riffle project is located just upstream of Cypress Street which was previously described in this blog: http://calsport.org/fisheriesblog/?s=painter.

Figure 2.  Rearing juvenile Chinook.  California Department of Fish and Wildlife photograph.

Figure 2. Rearing juvenile Chinook. California Department of Fish and Wildlife photograph.

The completed restoration provides up to 1.48 acres of new side-channel rearing habitats at the minimum Keswick Dam release of 3,250 cfs (Figure 3).  The restoration included installation of numerous large woody debris structures to increase the habitat complexity for young Chinook.  Video footage of the project by John Hannon is provided at:  Side Channel Projects

More such actions are planned for implementation on the upper Sacramento River in 2017 and years beyond.

Figure 3.  Post-construction schematic of the North Cypress side-channel project.  Restored side channels are depicted by blue lines (courtesy of the Western Shasta Resource Conservation District).  Sacramento River flow is from the upper right to the lower left in the photograph.

Figure 3. Post-construction schematic of the North Cypress side-channel project. Restored side channels are depicted by blue lines (courtesy of the Western Shasta Resource Conservation District). Sacramento River flow is from the upper right to the lower left in the photograph.

Department of Interior’s Central Valley Anadromous Fish Habitat Restoration Program

CVPIA 2017 Annual Work Plan Draft Cover Art

Over the past twenty-plus years, the US Bureau of Reclamation and the US Fish and Wildlife Service have implemented multiple actions to restore physical habitat for salmon and steelhead in the Central Valley.  While these agencies in the Department of Interior have focused much of their efforts on the tailwaters of Reclamation’s federal Central Valley Project dams (Shasta/Keswick, Whiskeytown, Folsom/Nimbus, and New Melones), they have implemented projects on other tributaries as well (e.g., Butte Creek).

The overall mandate and effort stems from the Central Valley Project Improvement Act (CVPIA) of 1992 and its sub-element – the Anadromous Fish Restoration Program (AFRP).  The Act established the Central Valley Project Restoration Fund (CVPRF or Restoration Fund), which includes the Trinity River Restoration Plan and the San Joaquin River Restoration Plan.  Funding comes from appropriations from the U.S. Congress, collections from water and power contractors, and non-federal cost-share obligations.  Funding varies annually – the federal share for 2017 projects is budgeted at $22 million.1  Total funding for Interior’s 2017 efforts in the proposed federal budget is approximately $55 million.  Major projects for 2017 include stream channel restorations and fish passage projects throughout the Central Valley.

With the changes that will come with the new federal government administration in 2017, we can expect many changes to the program, including funding.  Setting priorities and funding allocation for the coming year will be a complex process.  The state and federal goals and objectives may be in conflict.  The 2017 and coming years’ programs will help determine the future of Central Valley salmon, steelhead, sturgeon, American shad, and striped bass.

Commercial and sport fishermen will have to be especially vigilant.  The whole restoration process has so many components that often are uncoordinated.  Resource advocates should seek a stronger role in the process and come together in common purpose.  Let’s start by having a strong voice in the future of CVPRF and CVPIA-AFRP.

Suisun Bay Marsh Habitat

Wet years have led to high production of salmon, steelhead, smelt, sturgeon, splittail, shad, and striped bass in the Central Valley and Bay-Delta. One of main reasons for this high production is that Suisun Bay and Marsh habitat come into play in winter and spring when freshwater dominates the area under high Delta outflows.

High flows from winter-spring storms carry the young of these species from rivers and the Delta into the Bay. Longfin and Delta smelt even spawn in the Bay and adjacent Napa River. In my own personal experience1 surveying the area in winter-spring of the wet years 1978 and 2006, I observed very high use by young of these species, indicating the area’s high importance as a rearing area for estuarine and anadromous fishes. My experience mirrors that of 35 years of study in the Marsh by Peter Moyle at UC Davis.2

Even in dry years, moderate winter Delta outflow from infrequent winter storms pushes freshwater and young anadromous and estuarine fishes into Suisun Bay/Marsh. Rearing in the Bay and Marsh favors survival of juvenile fish for many reasons, chief among them shallow turbid freshwater that provides abundant food, cool waters through spring, and protection from predators. Fish in the Bay and Marsh also have greatly reduced risk of being lost in the interior Delta to poor habitat, abundant predators, the export pumps, and other water diversions.

Once young fish get to the Bay, they grow quickly and become gradually more tolerant of brackish waters that return after the storms. Salmon, steelhead, longfin smelt, and sturgeon make a full transition and move to the lower Bay and ocean. The Delta smelt, splittail, and striped bass remain in the brackish water through the summer and fall, taking advantage of abundant food and the cooler waters of the Bay. No other region offers these advantages and necessary habitat conditions to the anadromous and estuarine fish species of the Central Valley and Bay-Delta.

Efforts have been ongoing for several decades to restore habitat in Suisun Bay-Marsh. Most recently, the restoration has come under the wing of the State Resources Agency’s EcoRestore program with several new projects, most notably the Tule Red project along the north shore of Grizzly Bay (Figure 1). Other potential sites include Wheeler Island, Chipps Island, and Winter Island, in part by including existing duck hunting clubs under active management. These three sites should be actively pursued by EcoRestore, because they could be restored to tidal marsh. Under existing conditions, their low levees are often overtopped during high winter tides in storm surges, allowing young salmon to enter. However, these fish become trapped when water levels drop. Opening these habitats to the tide would provide new habitat and eliminate stranding.

Figure 2 shows a flooded Wheeler Island. The Collinsville area offers many restoration options including Montezuma Island, the old Navy base, and the old PG&E power plant site. Managed wetland areas adjacent to Montezuma Slough within the Marsh offer many opportunities for tidal habitats along the slough (Figure 3). Among all the above opportunities, only Tule Red is included in EcoRestore (Figure 4). EcoRestore should take greater advantage of the existing high value of Suisun Bay-Marsh habitats and the high potential benefits per unit cost of projects in this area compared to other planned projects upstream in the Delta and Valley.

Returning to where this article started, fish need the winter and spring flows to get them to Suisun Bay-Marsh and to sustain them. Even the driest years have winter storms that partly accomplish this despite the capture of most dry year the rain and snowmelt in Valley reservoirs. Thus, dry year storm pulses become so essential. The state and federal water projects in the Delta also covet these storm pulses and divert significant parts of them through the Delta pumps. The proposed Twin Tunnels would take even bigger bites out of dry year storm pulses3 before they are “lost” to the Bay and ocean. Instead, storm pulses should be enhanced in drier years by allowing a reasonable amount of Valley reservoir inflows to pass through the reservoirs and by limiting diversions of storm pulses from the Delta.

Figure 1. Recommended restoration sites in Suisun Bay. CSPA owns 14 acres along the shoreline near Collinsville below the number 6. (Basemap Source: Suisun Marsh Plan)

Figure 1. Recommended restoration sites in Suisun Bay. CSPA owns 14 acres along the shoreline near Collinsville below the number 6. (Basemap Source: Suisun Marsh Plan)

Figure 2. Flooded Wheeler Island on north shore of Honker Bay. Island levees breached in 2005 and have been marginally repaired. Without active management such sites may become permanently breached and actively eroded. See Figure 1 for location. (Source: GoogleEarth)

Figure 2. Flooded Wheeler Island on north shore of Honker Bay. Island levees breached in 2005 and have been marginally repaired. Without active management such sites may become permanently breached and actively eroded. See Figure 1 for location. (Source: GoogleEarth)

Figure 3. Habitat map of Suisun Bay/Marsh. (Source: Suisun Marsh Plan)

Figure 3. Habitat map of Suisun Bay/Marsh. (Source: Suisun Marsh Plan)

Figure 4. EcoRestore projects. (Source: http://resources.ca.gov/ecorestore/ )

Figure 4. EcoRestore projects. (Source: http://resources.ca.gov/ecorestore/ )

 

  1. Cannon, T. and T. Kennedy, 2007. Fish Use of Shallow Water Habitats of the Western Delta 1978-79 and 2002-07, May 2007.
  2. https://californiawaterblog.com/2011/07/28/the-future-of-suisun-marsh/
  3. The Tunnel proposal does recognize the importance of the storm pulses for the Bay and would allow some of the first pulse to pass.

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: http://www.youtube.com/watch?v=BP_szST5REo&NR=1
  • School of juvenile Chinook salmon rearing behind a Lake Redding bridge pier in the Sacramento River at water depths approximately 10 feet deep: https://youtu.be/g0dFA8V4-sc
  • 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: https://youtu.be/Tv0TtOCdzNY
  • 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: https://youtu.be/uAT9Wkx-nSY

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. http://www.dfg.ca.gov/fish/Resources/HabitatManual.asp

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. http://www.westcoast.fisheries.noaa.gov/publications/recovery_planning/salmon_steelhead /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.
http://www.nmfs.noaa.gov/stories/2016/02/docs/sacramento_winter_run_chinook _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. https://www.fws.gov/lodi/anadromous_fish_restoration/documents/WorkingPaper_v1.pdf

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. https://www.fws.gov/cno/fisheries/CAMP/Documents/Final_Restoration_Plan_for_the_AFRP.pdf

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. http://www.norcalwater.org/wp-content/uploads/2011/07/vogel-final-report-apr2011.pdf