Given the critical role of the streamflow regime for instream, riparian, and floodplain ecosystem sustainability, modeling the long-term effect of urbanization on streamflow is important to predict possible changes in stream ecosystems. Since flow duration curves are largely used to characterize the streamflow regime and define indices for stream ecosystem health, a stochastic model is presented that links the key physical features of urbanizing basins with rainfall variability to determine the resulting flow duration curves. The model is tested against 11 basins with various degrees of urban development, characterized by the percentage of impervious areas in the basin. Results show that the model is able to reproduce accurately the entire flow duration curve. The analysis performed suggests that the transformation of green (i.e., water used in evapotranspiration) to blue (i.e., streamflow) water in urbanizing basins is an important long-term source of ecohydrological alteration.