Assessment of Spring Chinook Salmon Habitat Suitability in the San Joaquin River Using a 2-D Depth-Averaged Model

Abstract

The San Joaquin River Restoration Program (SJRRP) provides adult Chinook salmon with a passage to upstream spawning beds and a safe route for juveniles returning to the Delta. A two-­‐‐ dimensional depth-­‐‐averaged hydrodynamic model based on the RMA10 scheme was developed to simulate the hydraulic properties (current velocities, depth, water surface elevation) of three proposed alternative migration pathways to explore flow patterns and offer useful insights into the effects of hydrodynamic alterations of the channel, a critical capability for determining the best passage for migration. The finite element model reasonably described the hydrodynamic conditions and calculated a Suitability Index (SI) for the habitat for spring-­‐‐run Chinook salmon, with a Nash-­‐‐ Sutcliffe Coefficient (NSC) of 0.75 for discharge and 0.56 for water surface elevation (WSE) respectively. The alternatives analysed were found to be characterized by similar SI distributions under the same boundary conditions. Alternatives 2 and 3 had higher overall Weighted Area Habitat Suitability Index (WAHSI) values and would thus be expected to provide better environments for salmon migration than Alternative 1. Normalized cross-­‐‐ correlation calculations revealed fair correlations between the WAHSI values and upstream discharge or downstream water surface elevation. The hydrodynamic model may also provide a reference for similar suitability studies of salmon habitat in other inland rivers.