Biological organisms can pose a threat to water quality and can be responsible for waterborne diseases. Because it is very expensive and time consuming to test for each pathogenic organism, coliform bacteria and E. coli, which originate in environmental and animal sources, serve as good pathogenic indicator organisms. This study focused on evaluation of water quality in New Jersey water bodies by monitoring both E. coli and coliform using different methods. Water samples were taken over two months at different sites. Three different methods used in this study are membrane filtration, PetrifilmTM and IDEXX methods to compare and determine which one or in combination methods are the most efficient and reliable way to identify and quantify bacterial contamination. It was concluded that areas that were highly urbanized, specifically high urban and agriculturally developed areas, had an increased level of contamination. Our study suggested that modified membrane filter method in combination of IDEXX Colilert® System provide the best results. Further research, such as Microbial Source Tracking (MST), will be conducted to identify the origin of fecal contamination.