In much of the world, rapidly expanding areas of impervious surfaces due to urbanization threaten water resources. Although tools for modeling and projecting land use change and water quantity and quality exist independently, to date it is rare to find an integrated, comprehensive modeling toolkit to readily assess the future course of urban sprawl, and the uncertainties of its impact on watershed ecosystem health. We have developed a combined socio-economic-ecological toolbox, running on the ArcGIS platform, to analyze subsequent impacts on streamflow and nutrient export using the spatial pattern of urbanization in response to anticipated socio-economic conditions and scenarios. We have applied our toolbox to two New York State catchment areas, Onondaga Creek watershed and Wappinger Creek, that have undergone rapid development in the last decades. Uncertainties in temporal trends of new housing permits, spatial distribution of development detection and development potential, and stream conditions were evaluated using three separate toolsets (ArcECON, ArcGEOMOD, and ArcGWLF, respectively). The toolbox capabilities are demonstrated through a year 2020 scenario prediction and analysis, where the aforementioned tools were explicitly linked to determine future housing development, spread of impervious areas, runoff generation, and stream nitrate flux. Higher economic growth was estimated to induce increased new housing permits and spread of impervious surface areas, leading to flashier streamflow as well as worsening stream condition, which was aggravated when only the forest lands were allowed to be developed.