The majority of people in developing nations rely on untreated or minimally treated surface and shallow groundwater sources which are prone to faecal contamination. This study evaluated the utility of EC 3M Petrifilm and sanitary inspection forms (SIFs) as tools to assess 47 water sources and identify hazards of contamination in two rural Ugandan villages (90% were surface sources). Water samples were cultured on EC 3MTM PetrifilmTM, which are intended to enumerate E. coli and total coliforms following 24 h incubation at 37 ºC. Isolated bacteria were cultured on MacConkey agar and identified using standard biochemical tests, while selected isolates were verified by sequencing 16S rRNA genes. From 105 Petrifilms, 110 presumptive E. coli were isolated and identified to genus level. However, only 33 presumptive E. coli isolates from 14 water sources (representing 27 distinct strains as determined by PFGE) were confirmed E. coli. The other presumptive E. coli isolates were identified as Citrobacter, Enterobacter, Proteus, Salmonella, and Yersinia species. SIFs used an adapted survey designed for urban water sources of Uganda. The form yielded a SIF score based on binary data and characterized potential sources of contamination. SIF scores alone offered little information to distinguish between contamination levels of surface water sources, but the information collected in the surveys could be used to identify ways to improve sources. The results of this study suggest that the use of sanitary surveys may assist in identifying potential pollution sources that may be targeted to protect water sources. Bacterial monitoring using EC 3MTM PetrifilmsTM may be effective for the screening of relative levels of contamination of source waters, including surface sources.