4.2.4. Model setup

originates mainly from snowmelt and runoff in the high Sierra Nevada, eventually converging with the Sacramento River in the Sacramento-San Joaquin Delta in Northern California. The SJR has experienced considerable low flow over the years, at times ceasing to flow completely. Chinook salmon was historically abundant in the SJR, but their populations have significantly decreased due to the insufficient flow. In order to restore and sustain salmon and other fish populations, the San Joaquin River Restoration Program (SJRRP) was established in 2006 to maintain continuous flow along the entire length of the river and improve its hydrodynamic conditions from Friant Dam to its confluence with the Merced River. Suitable hydrodynamic conditions, including flow velocity and water depth, are crucial for the safe passage of migrating salmon. Due to practical limitations, the flow has been rerouted along several alternative pathways specifically designed and created as part of the river restoration effort, modifying the traditional SJR channels. These alternatives were designed and compared to support the passage of fish by providing adequate hydrodynamic conditions throughout the river reach. The first objective of the research conducted for this case study was to model the stream conditions, including current velocity, depth, and WSE, for three alternatives proposed for the SJRRP given the same hydrologic/hydraulic boundary conditions. This part of hydrodynamic research has been done and published [28]. The second objective was to further investigate how the water quality at the upstream of the SJR affects the downstream. A 2D water depth-integrated water quality model was developed corresponding to the previous hydrodynamic model to simulate and predict the fate and transport of the contaminants in the upper SJR reach. The water quality

Figure 9. Spatial distribution of water temperature at 12:00 am on Julian day: (a) 180, (b) 190, (c) 200, and (d) 210.

model will provide a tool for the SJR restoration and management in the future.

The study area covered approximately 90 river kilometers from the SJR monitoring station near Dos Palos (SDP) to the SJR monitoring station at the Fremont Ford Bridge (FFB) near California Highway 140, which is located within the Middle San Joaquin-Lower Chowchilla

4.2.2. Investigation domain and model mesh

104 Applications in Water Systems Management and Modeling

A vertically integrated hydrodynamic model has been employed using the finite element scheme RMA10 to simulate flow velocity, water depth, and WSE. The governing equations were Eqs. (5)–(8). Compared with the first case study, the Coriolis force and wind stress are insignificant and can thus be neglected for this small-scale river reach. For the initial conditions, the river was assumed to be at rest at the beginning and it took a considerable time (10 days) to reach the actual initial conditions. The boundary conditions included the upstream flow rates, the known downstream WSEs, no leakage across the surface and the bottom, a drag stress at the river bottom, no wind stress and zero pressure at the water surface.
