The safety of land application of manure and the potential for food and water contamination by pathogens from agricultural runoffs have been the concern of many groups throughout the world. Their origin has been both point and non-point sources to most watersheds. Their fate and transport in watersheds supplying drinking water, from their deposit in feces and manure originating from Concentrated Animal Operations to their dispersion in major creeks is poorly understood. Multiplex fluorogenic PCR was used in conjunction with plate counts to quantify fate of E. coli O157:H7 in soil, manure, feces, and dairy washwater. The death of the majority of E. coli O157:H7 in soil takes place as a fast exponential decay. After a few weeks, the initial purely exponential decay of the killing curve changes to a more complex, slowly decreasing function. After 60 days a small fraction of the cells survived, and this fraction may be important factor in re-contamination of the environment or re-infection of cattle.