Groundwater pumping is a boundary condition in groundwater models, and surface application, reuse, diversions, and water reclamation plant discharges are boundary conditions in hydrologic or hydraulic (i.e., surface) models. These processes can be simulated, however, as internal flow and solute transport components within a fully integrated groundwater–surface water model. A methodology has been developed and incorporated into the MODHMS fully integrated surface–subsurface modeling framework to enable evaluation of water distribution and application and impacts to water quality on surface and subsurface domains. This methodology allows the supply and delivery of water and associated water quality to be a part of the model solution rather than being predetermined boundary conditions to the system. Furthermore, this methodology handles temporal and spatial changes to land use and water quality and associated effects on outdoor water distribution, infiltration, runoff, and evapotranspiration properties that are related to surface cover or land use classifications. This new methodology was applied to a portion of the Upper Santa Clara River system and underlying groundwater basins of southern California to aid in the evaluation of a Cl− total maximum daily load (TMDL) study. The outcome of this modeling evaluation has led to an enhanced understanding of how Cl− is transported throughout the surface–subsurface model domain and improved collaboration among stakeholders. The model serves as a powerful tool with which to develop and evaluate various approaches for the Cl− TMDL implementation for the Upper Santa Clara River system.