Numerical modeling is an efficient and useful method for understanding the hydrodynamics and water quality responses to nutrient loading changes and other management in estuarine and coastal systems. In this study, the Environmental Fluid Dynamic Code (EFDC) was applied in the Famosa Slough, a small tidal marsh system in urban San Diego County, California, to analyze multiple management scenarios focusing on different aspects of controlling processes: watershed load reduction, macroalgae harvesting, dredging, and the combination of different options. In order to evaluate these management scenarios, a previous EFDC model was enhanced through modifying the model code to allow simulations of both benthic and floating macroalgae as separate state variables, and configuring a sediment diagenesis model to predictively represent the dynamic interactions between the watershed load and benthic nutrient flux. The model was calibrated and verified by comparing model predictions with the observed data of hydrodynamic and water quality parameters throughout 2008. The calibrated model was then applied to simulate the water quality response to various management scenarios. The simulated results showed that combining watershed nutrient load reductions and harvesting floating macroalgae can produce significant water quality benefits. The results provide useful information for hydrological ecosystem protection and can be used for determining cost-effective implementation actions in the future.