The methods reported in this paper identify swine and cattle fecal pollution in water using primers developed for specific toxin genes from Enterotoxigenic E. coli as the template for PCR. This research has determined the following: crossreactivity of the primers; detection limits for the toxin gene by molecular methods as compared to detection by plating of culturable E. coli in various water types; specificity of the biomarkers for a target sample; and, the minimum detection limit in various water types. Includes 21 references, tables.