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Chinook Salmon in the San Joaquin Valley: What are the Benefits of Riparian Restoration?

By Stacy Small and Tom Griggs

River Partners has a key role to play in the preservation and restoration of Central Valley salmon populations through our habitat restoration efforts. Riparian habitat and floodplains are of critical importance to salmon for breeding, juvenile rearing, and outmigration. Salmonids are highly adapted to the geomorphic and hydrologic features of meandering rivers, and the various features typical of valley rivers are related to specific aspects of the freshwater phase of their life cycle (Trush et al. 2000). Deep, cold pools function as adult holding areas leading up to spawning. Gravel beds in riffle areas serve as spawning sites. Juveniles and adults find shelter beneath undercut banks and near large wood contributed from riparian zones. Inundated floodplains and side channels provide high quality juvenile rearing habitat. Finally, riparian vegetation stabilizes streambanks, reducing erosion and capturing sediment that could otherwise run into a stream, increasing turbidity and clogging gravel spawning beds. Riparian vegetation provides a source of large wood that serves as shelter from predators and strong currents, hosts aquatic invertebrates for food, and traps and retains spawning gravel and organic detritus in the river system (Opperman and Merenlender 2007). Sticks and branches in the river disrupt the water surface and create “bubble curtains,” which create visual screens to provide juveniles protection from predators.

A recent survey of Mokelumne River spawning beds showed that large wood improved in-stream geomorphic features and that salmonids preferred to construct their redds near large wood pieces (Senter 2008). Living riparian vegetation along the streambank contributes large wood to the system as well as potentially trapping and retaining wood pieces as they pass downstream (Opperman and Merenlender 2007).

Figure 1: Fall-run Chinook spawner numbers for this decade in the San Joaquin River system. Preliminary data from California Department of Fish & Game.

Riparian restoration sites also can improve channel geomorphology and increase streambed complexity, which may result in better overall habitat conditions for salmon (Opperman and Merenlender 2004). Such streambed improvements may include gravel beds for breeding, increased sub-gravel water flow, and deeper coldwater pools for holding areas.

Overhanging vegetation provides shade, resulting in the cooler water temperatures required by spawning salmonids. Riparian vegetation also contributes important food inputs to the aquatic system, including terrestrial insects and vegetation detritus upon which aquatic invertebrates feed.

Riparian vegetation throughout the valley floor has been extensively cleared over the past century and in many places only occurs as narrow, intermittent strips along its banks. Current conditions make it unlikely for native vegetation to recruit without active intervention. Under natural conditions, cottonwood and willow seed dispersal is synchronized with receding river flows during late spring or early summer that expose mineral substrate (gravel and sand bars) ideal for seedling establishment. Currently, hydrographs (water flow patterns) of Central Valley rivers are typically managed in such a way that does not provide exposed mineral substrate (gravel and sandbars) at the appropriate time for cottonwood and willow establishment. Widespread competition from aggressive non-native plant species (Himalayan blackberry, tree of heaven, black walnut, and giant reed, to name a few), coupled with an altered hydrologic regime, also prohibits the establishment and survival of key riparian plant species. As a result, remnant riparian vegetation is senescing along many stretches of valley rivers, with no younger age class growing up in its place.

Aerial view of the Bear River levee setback restoration site. The swale, in the center of the curving rows, is planted with native grasses and rushes. Its design allows for fish access and egress. Photo by Tom Griggs.

To address this situation, River Partners has planted 6,000 acres of riparian habitat along Central Valley rivers in the past ten years, working in the San Joaquin and Sacramento River systems. To increase the amount of shaded riverine aquatic habitat and slow erosion, we have intentionally designed plantings near eroding river banks on some sites. On all of our restoration sites, we plant a diverse array of native woody plants (shrubs and trees) and herbaceous species configured in patterns intended to benefit both aquatic and terrestrial systems.

Floodplains have also been identified as a critical habitat feature for juvenile salmonid rearing. Floodplain characteristics include more hydrologic variability, greater water surface and shallow area, longer hydraulic residence times, and lower water velocities. These conditions result in warmer water temperatures that produce higher chlorophyll levels and more invertebrates. Sommer et al. (2001) found that, at the Yolo Bypass, juveniles that foraged on inundated floodplains exhibited faster growth rates and increased feeding rates. Higher prey availability in floodplain environments could mean improved physical condition and higher juvenile survival for salmon reared in these locations.

Through human engineering, river channels have been disconnected from their floodplains over time by a network of levees and canals throughout the valley. In addition to planting riparian vegetation, River Partners is incorporating design elements into our restoration plans to improve floodplain conditions for salmon throughout the Central Valley. Along the Bear River in Yuba County, we have collaborated on a levee setback project and construction of a low swale that will allow young salmon floodplain access and egress (see photo, above). The swale has been planted with native wetland plants and willows along it upper banks, to provide multi-species benefits for migratory songbirds like Common Yellowthroat, Yellow Warbler, and Blackheaded Grosbeak. At our LaBarranca restoration site on the Sacramento River National Wildlife Refuge, old gravel mining pits will be filled to prevent fish entrapment on the floodplain. On the San Joaquin River National Wildlife Refuge, levee breeches are planned in such a way that will optimize drainage after large flood events, to allow fish to enter and exit the floodplain. Concurrently, we have constructed and vegetated high-ground refugia (“bunny mounds”) and vegetated levees on the Refuge as flood escape sites for terrestrial wildlife such as the endangered riparian brush rabbit.

However, what will happen in dry years? In the face of drastic salmon declines, will river flows be managed in such a way as to inundate designated floodplains during this critical period of juvenile salmon rearing? Will active riparian and floodplain restoration be integrated as a primary tool in salmon restoration programs? These and many other questions should be asked as we reexamine the management of freshwater ecosystems for the benefit of Central Valley salmon populations.


Opperman, J. J., A.M. Merenlender. 2004. The effectiveness of riparian restoration for improving instream fish habitat in four hardwood-dominated California streams. North American Journal of Fisheries Management 24:822-834.

Opperman, J. J., A.M. Merenlender. 2007. Living trees provide stable large wood in streams. Earth surface processes and landforms 32:1229-1238.

Senter, A. 2008. Geomorphic and Ecological Interactions of Large Wood and Pacific Salmonid Redds Across Habitat Units in the Mokelumne River. 26th Annual Salmonid Restoration Conference, Lodi, CA.

Sommer, T. R., M.L. Nobriga, W.C. Harrell, W. Batham, W.J. Kimmerer 2001. Floodplain rearing of juvenile chinook salmon: evidence of enhanced growth and survival. Can. J. Fish. Aquat. Sci. 58:325-333.

Trush, W. J., S.M. McBain, and L.B. Leopold. 2000. Attributes of an alluvial river and their relation to water policy and management. PNAS 97:11858-11863.

Yoshiyama, R. M., E.R. Gerstung, F.W. Fisher, P.B. Moyle. 1996. Historical and present distribution of chinook salmon in the Central Valley drainage of California. Pages 309-362 Sierra Nevada Ecosystem Project: Final report to Congress , Vol. III, assessments, commissioned reports, and background information. University of California Centers for Water and Wildland Resources, Davis, CA.

The above article originally appeared in the Summer 2008 issue of the River Partners Journal.