Culturable faecal coliform, epidemic, clinical, faecal and recreational beach enterococci strains possessing putative virulence genes were enumerated over the course of 5 weeks to comparatively assess their persistence in tropical marine and fresh waters. For the clinical and epidemic strains tested, it took 2.38 ± 0.45 days for a 1-log reduction (T₉₀) in marine water. A higher T₉₀ average of 2.51 ± 0.08 was observed for the commensal and environmental strains. Generally, lower T₉₀ values of 2.14 ± 0.26 and 2.15 ± 0.16 days respectively were observed for hospital and community acquired enterococci strains in fresh water mesocosms subjected to tropical ambient temperature. Beach water enterococci and enterococci recovered from faeces of humans survived for up to 20 days and 23 days respectively in fresh and marine waters. The epidemic strain, MMH594, an esp-positive clinical bacteremia isolate that previously caused multiple infections in a hospital ward outbreak fares favourably well in tropical marine and fresh aquatic environments. For enterococci, the decay rate was approximately 13% higher in fresh water than was observed for marine water. On the contrary, for E. coli, the decay rate was approximately 17% lower in fresh water than was observed in marine water. Generally, the whole, the population trends of E. coli and enterococci in fresh and marine water mesocosms did not reveal any evidence of growth. Our findings suggest that potentially pathogenic bacteria can resume active growth after three weeks of being harboured by the reservoir-beach sand and still pose threat to public health.