This study explores the application of the Watershed Modelling System (WMS) and the Gridded Surface Subsurface Hydrologic (GSSHA) model to develop sediment transport and water quality models for Austin’s urban watersheds, with the aim of enhancing the city's flagship environmental monitoring program, the Environmental Integrity Index (EII). As Austin faces growing urbanization and associated environmental challenges, it becomes crucial to assess and manage the health of its urban creeks. The WMS and GSSHA models are employed to simulate hydrological processes, including runoff, sediment and pollutant transport, and water quality dynamics, within the city's watersheds. These models integrate land use, topography, soil type, and land cover with surface and subsurface hydrology to provide a comprehensive representation of water quality under various land use and weather conditions. The results from the sediment and water quality models are incorporated into the EII framework, enabling a detailed evaluation of watershed conditions, pollutant loads, and the impacts of urban development. This expanded tool will support decision-making for urban planning, environmental protection, and the sustainable management of Austin’s urban water resources, ultimately contributing to the restoration and preservation of water quality in the city's creeks.