Impairment of rural streams and receiving lakes as a result of microbial pollution has a significant impact on human health and quality of life. Contaminated drinking water supplies and the closure of recreational surface waters are two common consequences of microbial pollution. Many aspects of microbial survival and transport are poorly understood. For example, it is evident that stream sediments provide an environment suitable for the extended survival and possible growth of fecal microorganisms. Several watershed-scale studies have alluded to the presence of a reservoir of fecal microorganisms within stream sediments, but have not been able to quantitatively identify the relative contribution of this source to water quality degradation under varying hydrologic and environmental conditions. For areas of degraded water quality with many potential sources, understanding these processes is critical if appropriately directed watershed management plans are to be implemented. In this study, a combination of field experiments and mathematical modeling was used to elucidate the processes which control the fate and transport of enteric bacteria in alluvial streams. The overall objective of the research was to further the development of microbial water quality models. A tracer bacterium, 'Escherichia coli' NAR, was used to investigate the survival, resuspension, advective-dispersive movement, and settling of sediment-associated bacteria in several natural alluvial streams. This study has illustrated that enteric bacteria can survive in bed sediments for up to 6 weeks. Inactivation of the tracer-bacteria within bed sediments of the majority of the streams studied resembled typical first order decay. However, in the nutrient-rich bed sediments in Carroll Creek, ON, Canada, where water temperatures were typically lower than 16°C, the inactivation of the tracer-bacteria did not follow a first order decay. The number of tracer-bacteria within the stream bed did not decrease for the first five days of the experiment. Results from a detailed monitoring study conducted in Swan Creek, ON, Canada has provided information pertaining to the resuspension of sediment-associated bacteria due to natural hydrologic influences. Critical conditions for resuspension, as well as resuspension rates, of sediment-associated bacteria were determined for several storm events. Field experiments and mathematical modeling were used to determine dispersion coefficients, deposition rates, and partitioning coefficients for sediment-associated bacteria in two natural streams. The results provided evidence that bacterial adsorption can be modeled as an irreversible process in freshwater environments. Calibrated net settling velocities of sediment-associated bacteria were found to be comparable to literature values for fine sediments. The information presented in this study will further the development of representative microbial water quality models. Recommendations for improving current microbial water quality models, and for future research have also been outlined.