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, we present two stochastic models, with different levels of complexity, that link the key physical features of urbanized basins with rainfall variability to determine the resulting flow duration curves. The two models are tested against 11 basins with various degrees of urban development, characterized by the percentage of impervious areas in the basin. Results show that the more complex model needs to be used 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 urbanized basins is an important long-term source of ecohydrological alteration. The modeling scheme also provides useful links between rainfall variability, urbanization levels, and some streamflow indices of high and low flows.