Eutrophication of the San Joaquin River (SJR) has resulted in low dissolved oxygen (DO) conditions, which has led to a regulatory response and development of total maximum daily load (TMDL) allocations. Due to the dynamic nature of processes governing oxygen depletion in the SJR, a model was needed to help stakeholders understand the fate and transport of nutrients and oxygendemanding substances that cause the low DO conditions. Here, the Watershed Analysis Risk Management Framework (WARMF) model was used to simulate nutrient removal and control strategies, accounting for the secondary effects of growth and transformation between sources and discharge. Using the management alternatives in the WARMF Consensus Module, simulations were run to test the global removal of nutrient inputs on downstream phytoplankton growth, a major contributor of oxygen demand in the SJR. In the simulations, removal of ammonia had the greatest impact on downstream phytoplankton, causing a 32% reduction, while removal of phosphate and nitrate caused reductions of 25% and 13%, respectively. When ammonia and nitrate were both removed, phytoplankton reduction was 62%. These model results suggest that nitrogen control programs would be more effective than phosphorus programs. Using the Data Module in WARMF, input files were modified to determine the impacts of individual tributaries and agricultural drainages. In each simulation, the contributing loads for individual inputs were removed while maintaining flow. According to the model output, the largest impact on phytoplankton occurred with the removal of mass loads from Salt Slough (32% less than baseline). The effect of removing the mass loads from Mud Slough had a slightly lower impact (26% less than baseline). The WARMF model proved useful for exploration of planning and management alternatives, providing an expert decision-making tool that is available to stakeholders
