Escherichia coli was used as a bacterial tracer for the development, calibration, and validation of a watershed scale fate and transport model to be extended to a suite of reference pathogens (Cryptosporidium, Giardia, Campylobacter, E. coli O157:H7). E. coli densities in water and sediments from the Blackstone River Watershed, Massachusetts, were measured at three sites for a total of five wet weather events and three dry weather events covering three seasons. The confirmed E. coli strains were identified by ribotyping for tracking the sources of E. coli and for determining the association of downstream E. coli isolates with isolates from upstream sediments. A large number of downstream samples were associated with upstream sediment sources of E. coli. E. coli densities ranged from 71 to 6,401 MPN ⁄ 100 ml in water samples and from 2 to 335 MPN ⁄ g in sediments. Pearson correlation analysis revealed significant correlations between E. coli and total coliforms in water (r = 0.777, p < 0.01) and sediments (r = 0.728, p < 0.01). In addition, E. coli concentrations in water were weakly correlated with sediment particle size and sediment concentrations (r = 0.298, p < 0.01). A hydrologic model, WATFLOOD ⁄ SPL9, was used to predict the temporal and spatial variation of E. coli in the Blackstone River. The rapid rise of stream E. coli densities was more accurately predicted by the model with the inclusion of sediment resuspension, thus demonstrating the importance of the process.