Male specific coliphages have been used as indicators of fecal contamination. Currently, the US Environmental Protection Agency (USEPA) is also evaluating the usefulness of this microbial indicator as part of the Ground Water Rule. There is a need to better understand the survival characteristics of this organism since their persistence in groundwater will ultimately dictate whether these organisms can be reliably detected. The survival of the male specific bacteriophage, MS2 was studied in 17 different groundwater samples that were collected from two vulnerable aquifers along a 50-mile stretch of the United States- Mexico border. The groundwater samples had varying chemical composition in terms of pH, total dissolved solids, chloride and nitrate content. There were significant differences in the inactivation rate of the MS2 bacteriophage in the different groundwater samples. The inactivation rates ranged from 0.4 log PFU/ml/day to as high as 1.8 log PFU/ml/day. No statistical correlation or relationship was observed between the chemical components of the groundwater sample (pH, TDS, chloride content, nitrate content) and the inactivation rates. The results suggest that the microbial ecology of the groundwaters is a critical factor controlling the persistence of male specific coliphages. Importantly, the results imply that the survival of male-specific coliphages cannot be assumed to show similar patterns or trends even in geographically related locations. Thus, results from groundwater monitoring programs should take the microbial ecology of the organism into consideration when interpreting occurrence data. Includes 9 references, tables.