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Pathogens from livestock and poultry manure are key sources of water, soil, and air pollution. The trend toward confinement animals feeding operations has increased the risk of the ecosystem pollution. The potential presence of pathogenic or disease-producing organisms in wastewater runoff was detected by using indicator organisms. Indicator organisms are general and larger groups of organisms that are easily counted. Fecal coliform, serve as an example of indicators bacteria that can be identified and enumerated easily in wastes. Fecal coliform are bacteria commonly found in animal manure. They are a subset of a large group of organisms know as coliform bacteria. This research investigated the presence of pathogens at a local swine farm to determine microbial concentrations in soil from the swine lagoon due to run-off, accidental spills on the property, and use of the water for field irrigation. The Membrane Filter Method for sewage sludge is used to analyse Total coliform and Eschrichacoli. This study included soil testing and microbial profiling of pathogen concentration using GIS mapping. The results from the laboratory experiments showed high levels of total coliforms and E.coli in areas around the lagoons and in the cropped field. This is an indication that there could be significant presence of pathogens in these areas. The results indicate that bacterial levels were not effectively reduced by on-site treatment.