Category Archives: Restoration

How do we increase salmon runs in 2018 and beyond?

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Over the past few months, I wrote posts on the status of specific runs of salmon in rivers throughout the Central Valley. In this post, I describe the overall status of salmon runs and the general actions to take to increase both escapement and fish available for commercial and sport harvest.

It was just over a decade ago that there were nearly one million adult salmon ascending the rivers of the Central Valley (Figure 1). At the same time, there were a millions more Central Valley salmon being harvested each year in sport and commercial fisheries along the coast and rivers of the Central Valley. Improvements in salmon management in the decade of the 1990s by the Central Valley Project Improvement Act, CALFED, and other programs had paid off handsomely with strong runs from 1999 to 2005. New and upgraded hatcheries, along with trucking hatchery smolts to the Bay, significantly increased harvest and escapement to spawning rivers.

Figure 1. Central Valley salmon runs from 1975 to 2016 including fall, late fall, winter, and spring runs. Source of data: CDFW GrandTab.

By 2008-2009, escapement had fallen by over 90% to a mere 70,000 spawners of the four races of salmon.  Fishery harvests were greatly restricted by 2008.  The winter run, the most threatened of the four runs fell from 17,296 to 827 spawners in just five years.  Drier years from 2001-2005, poor ocean conditions in 2004-2005, record-high Delta water diversions, and the 2007-2009 drought were contributing factors in the declines.  Impacts to coastal communities and the fishing industries were severe.

Extraordinary recovery measures included closing fisheries and trucking most of the hatchery smolt production to the Bay or Delta.  Federal salmon biological opinions (2009, 2011) limited winter-spring water-project exports from the Delta.  Hundreds of millions of new dollars were spent on habitat and fish passage improvements in the Valley to increase salmon survival and turn around the declines in runs.  A look at Figure 1 indicates that these efforts proved effective in limiting run declines from the 2012-2015 drought compared to the 1987-1992 and 2007-2009 droughts.

However, the prognosis for the future is again bleak, especially for wild, naturally produced salmon.  The consequences of the 2012-2015 drought  have not fully played out.  Once again, projected runs are low, and harvests are likely to be restricted.  Actions are needed to minimize long-term effects and to help bring about recovery of wild salmon productivity and fisheries in general.

Actions for 2018:

  1. Reduce harvest: Sadly but necessarily, the Pacific Fisheries Management Council and states are likely to take this first step of– restricting the 2018 harvest in the ocean and rivers to protect wild runs.
  2. Improve spawning, rearing, and migrating conditions: Sadly, this past year’s rearing and migrating conditions in the Sacramento River were unnecessarily compromised.   Water temperature at Red Bluff reached above the 56oF prescribed in the biological opinion and Basin Plan.  The higher temperatures resulted from low Shasta Reservoir releases (less than 5000 cfs – Figure 2) despite a virtually full Shasta Reservoir.  The low flow and higher water temperatures likely affected salmon egg incubation, rearing, and emigration-immigration success.  Reservoir releases will be necessary to meet flow and temperature targets in all Central Valley rivers and the Delta.
  3. Limit Delta exports: Delta exports this past spring reached unprecedented highs not seen in recent decades, resulting in high salmon salvage rates at the Delta fish facilities (Figure 3).1 With high water supplies from this past wet water year 2017, there will be high exports again unless there are some constraints.  If anything, winter-spring exports should be reduced to allow salmon to recover.  April-May exports should be reduced, like they were in the 1990’s and 2000’s, to 1500 cfs.

Near term actions over the coming year:

  1. Transport hatchery smolts to Bay: The transport of millions of fall-run smolts from state hatcheries on the Feather, American, and Mokelumne rivers to the Bay provides higher rates of escapement and contributions to the fishery and low rates of straying.  Barge transport to the Bay offers potentially lower rates of predation and straying for federal hatcheries near Redding.
  2. Raise hatchery fry in natural habitats: Recent research indicates that rearing hatchery fry in more natural habitat conditions increases growth rates, survival, and contributions to escapement and fisheries.  Raising hatchery fry in rice fields is one potential approach.
  3. Restore habitats damaged by recent record high flows in salmon spawning and rearing reaches of the Central Valley rivers and floodplains: In nearly every river, habitats were damaged by the winter 2017 floods, requiring extraordinary repairs and maintenance to ready them again to produce salmon.
  4. Take further actions to enhance flows and water temperatures to enhance salmon survival throughout the Central Valley: Actions may include higher base flows, flow pulses, or simply meeting existing target flow and temperature goals.

In conclusion, managers should take immediate actions to minimize the damage to salmon runs from the recent drought and floods, using this past year’s abundant water supply.  They should avoid efforts to exploit the abundant water in storage for small benefits to water supply at the expense of salmon recovery, and should make every effort to use the water in storage for salmon recovery.

Figure 2. Upper Sacramento River flows and water temperatures in May 2017. The target water temperature for Red Bluff is 56oF. Source of data: USBR.

Figure 3. Export rate and young salmon salvage at South Delta federal and state export facilities in May 2017. The target export rate limit for May should be 1500 cfs. Source of data: USBR.

Sometimes it doesn’t take a lot of water.

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In a May 29 post, I discussed how a small diversion of cold water from the West Branch of the Feather River sustains the Butte Creek spring-run Chinook salmon, the largest spring-run salmon population in the Central Valley. In a May 8 post, I described how the Shasta River, despite its relatively small size, produces up to half the wild fall-run Chinook salmon of the Klamath River. In both examples, it is not the amount of water, but the quality of the water and the river habitat that matters. In the former case, man brought water to the fish. In the latter, man returned water and habitat to the fish.

While both examples are remarkable given the relatively small amount of water involved, the relatively small restoration effort required on the Shasta River and the minimal effect on agricultural water supply make it almost unique.

Just take a look at the present late May 2017 hydrology of the Klamath River (Figure 1). There was only 140 cfs flowing in the lower Shasta River. At the same time, there was 25,000 cfs flowing in the lower Klamath, 2000 cfs in the upper Klamath below Irongate Dam, and 2000 cfs in the Scott River. What is different is that most of the Shasta flow is spring fed, some of which is sustained through the summer. Of the roughly 300 cfs base flow in the river in late May 2017, about 200 was from springs (Figure 2). By mid-summer, flow out of the Shasta River into the Klamath will drop to about 50 cfs, with agricultural diversions from the Shasta at about 150 cfs. October through April streamflow is generally sufficient to sustain the fall-run salmon population. Summer flows are no longer sufficient to sustain the once abundant Coho and spring-run Chinook salmon.

Figure 1. Lower Klamath River with late May 2017 streamflows in red. Note Shasta River streamflow was only 140 cfs near Yreka, California. Data source: CDEC.

Figure 2. Selected Shasta River hydrology in late May 2017. Roughly 150 cfs of the 300 cfs total basin inflow is being diverted for agriculture, with remainder reaching the Klamath River. Red numbers are larger diversions. The “X’s” denote major springs. Big Springs alone provides near 100 cfs. Of the roughly 100 cfs entering Lake Shastina (Dwinnell Reservoir) from Parks Creek and the upper Shasta River and its tributaries, only 16 cfs is released to the lower river below the dam. Red numbers and arrows indicate larger agricultural diversions. Up to 15 cfs is diverted to the upper Shasta River from the north fork of the Sacramento River, west of Mount Shasta.

Shasta River Fall Run Chinook Salmon – Status and Future

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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

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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

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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.