Seasonally managed wetlands in the San Joaquin River (SJR) watershed in California provide important benefits to wildlife and humans but are threatened through anthropogenic activity. Wetlands in the SJR are subject to salinity regulation, which poses challenges for wetland management. Salinity management in the SJR basin is supported by a process-based model, the Watershed Analysis Risk Management Framework (WARMF). Wetlands are simulated with a “bathtub” analog where water levels are assumed to be the same over one model compartment and the storage volume depends on depth. The complexity and extent of hydrological features pose challenges for input data acquisition. Two approaches to estimating inflow and pond depth and determining water sources were assessed. Approach 1 used mostly monitored data, while Approach 2 used wetland manager knowledge. Approach 2 predicted outflow and salinity better than Approach 1, and an important benefit was the simulation of water reuse within the wetland complex, which was previously not implemented. Approach 1 is generally suited for estimating pond depth when a model compartment represents one wetland, while Approach 2 is suited for wetlands with large spatial extent, many hydrological features, and managed flows. The improved model will support wetland management.