Predicting in-stream pathogen levels has long been known to be a challenging problem due to complex interactions between microorganisms and the natural stream environment, and the spatial heterogeneity involved in stream networks of a watershed. Here we have developed models for predicting E. coli (a pathogen indicator) in streams. In E. coli estimation, the first modeling approach uses Geographic Information Systems (GIS) based watershed indexes considering the undisturbed land cover, which encompasses the natural land cover area, wetlands, and vegetated stream corridors, and the disturbed land cover extent which includes areas receiving manure from confined animal feeding operations, tile-drained areas, and areas under cropped and urban land cover. The second approach involves developing mathematical models for calculating E. coli resuspension, deposition, in-stream routing, and growth in the streams. A hydrological model capable of predicting in-stream E. coli concentrations in the streambed sediment as well as in the water column was developed. In order to develop the hydrological model for predicting in-stream E. coli concentrations, firstly a model capable of predicting E. coli resuspension was formulated. Secondly, formulations for calculating in-stream E. coli routing, water temperature depended E. coli growth, and the streambed sediment and water column E. coli concentrations were developed. Finally, these formulations were programmed in FORTRAN language, and were integrated into the Soil and Water Assessment Tool (SWAT), a watershed scale hydrological model, written in FORTRAN. In addition to the model development, this study also involves monitoring E. coli concentrations in the streambed sediment and the water column xi extensively starting from May 2009 to December 2011 in the Squaw Creek Watershed, Iowa, USA. The observations were used to verify the model predictions, and results indicated that the models performed well. The GIS based approach developed here for estimating E. coli concentrations in streams can be potentially useful in predicting in-stream waterborne E. coli levels using watershed indexes. Approximately 95-98% of the predictions were within 1 order magnitude of the observed values, when we used hydrologically corrected watershed indexes for E. coli estimation. The model skills varied from 0.39 to 0.55. In E. coli resuspension model, approximately 81% of the predicted E. coli resuspension rates were within a factor of 2 of the inferred values (i.e., measured E. coli). All of the predicted resuspension rates were within a factor of 5 of the inferred values. The model skill value of 0.85 indicated that the model predicts E. coli resuspension rates successfully. The application of the modified SWAT model in the Squaw Creek Watershed, which was developed here, performed well. For example, approximately 62% of the predicted streambed sediment E. coli, and 82% of the predicted water column E. coli concentrations were within 1 order magnitude of the measured concentrations. The R 2 for month...