Fish Utilization of Habitat Features Incorporated into Levee Repairs on the Lower Sacramento River, California

Emergency levee repairs began in 2006 on the lower Sacramento River, California by the California Department of Water Resources. Three levee repair design types were developed and constructed to include specific habitat features, thus providing mitigation to meet the requirement of biological opinions issued by NMFS and USFWS. Our task was to evaluate how well the levee repair designs were working and what individual habitat features were important in terms of influencing fish use.

Using electrofishing methods, we related the occurrences of fry and juvenile Chinook salmon and bass predators to levee design type and habitat features at 15 repair and “Natural” sites (“Natural” in that they have not been engineered, are not rip-rapped, and are dominated by native, naturally established vegetation). We used generalized linear mixed models to analyze the data from the 15 sites, accounting for the fact that several points were electrofished at each site. 

Our results indicate that Chinook salmon fry were equally frequent at the Natural sites and the Bench/10:1 levee design type, which is a gradually sloping design type that can have benches. However, for Chinook salmon juveniles and bass predators, Dietl Ditch designs (engineered, off channel ditches running parallel to the channel), were best. Bass predators were least likely to be present at the Natural sites. Once we established relationships with design types, we turned to investigating habitat features.

Important habitat features for Chinook salmon fry and juveniles included submerged vegetation, instream wood, and shallower water depths. Chinook salmon fry were associated with finer substrates.  Unlike Chinook salmon, bass predators were associated with steeper bank slopes and coarser substrates. Bass predators exhibited positive relationships with instream wood measures. The relationships between instream wood and Chinook fry and juveniles, and bass, became stronger with greater water depths. 

We conclude that levee repair designs with habitat features could favor both Chinook salmon juveniles and bass predators; both are more likely to be present at the Dietl Ditch design type than others, increasing the chances of interaction and, potentially, predation. The shallower Bench/10:1 design type may benefit Chinook salmon fry and juveniles, and is less conducive to predators, particularly if submerged vegetation can provide additional habitat value.