Escherichia coli and Enterococcus are indicator bacteria that were measured in Iowa streams that drain land with different levels of swine production. We completed a study monitoring=g these bacteria over three and one-half years. Bacteria were readily transported from manured fields, reaching levels exceeding 10,000 per 100 ml of water. In contrast, long-term averages showed only a few hundred bacteria per 100 ml and long-term averages do not correspond to the estimated densities of swine in the three catchments. This and other data obtained from manured and non-manured fields suggest that wildlife are also a source. Cattle are also a likely source. Studies of E coli survival in soil suggest that avoiding manure application immediately before rainfall is a producer practice that will have immediate water quality benefits. This project also investigated the feasibility of using quantitative PCR to measure populations of Salmonella and E coli O157:H7, which are both human/livestock pathogens. While we were able to obtain qualitative measurements showing the presence of E coli O157:H7, the quantitation was not achieved.