Abstract: The two main rivers of southeast Texas: Guadalupe and San Antonio have shown high temporal increase in bacteria concentration during the last decade. The SPAtially Referenced Regression On Watershed (SPARROW) attributes model, developed by the U.S. Geological Survey (USGS), has been applied to predict the fluxes and concentrations of contaminants in unmonitored streams and to identify the sources of these contaminants. This model identifies every reach as a basic network unit to distribute the sources, delivery, and attenuation factors. The model is data intensive and implements nonlinear regression to solve the parsimonious relations for describing various watershed processes. This study explored watershed and hydrological characteristics (land uses, precipitation, human and animal population, point sources, areal hydraulic load and drainage density, etc.) as the probable sources and delivery mechanisms of waterborne pathogens and their indicator (Escherichia coli [E. coli]) in the Guadalupe and San Antonio River basins. The effect of using various statistical indices for model selection on the final model’s ability to explain the various E. coli sources and transport processes was also analyzed.