The large number of waterborne illnesses in Ireland and worldwide has highlighted the need to enhance strategies that minimize human exposure to pathogens in drinking water supplies. Waterborne pathogens of public concern together with relevant national and international legislation are reviewed in this study. Cryptospofidium species and pathogenic Escherichia coli are among pathogens of primary concern. The organisms originate from the gastrointestinal tract of animals and humans. They may be associated with persistent contamination of water sources, survive for long periods in the environment, and, in particular in the case of Cryplosparidium species, may survive in chlorinated water supplies. Prevention of waterborne infection should emphasize source protection in addition to water treatment. Risk assessment models can play an important role in protecting natural water systems from contamination with these pathogens. Qualitative approaches can provide an effective means of assessing risks with minimum resources and limited data; however, they lack the precision and predictive ability of fully quantitative approaches. Thirteen quantitative simulation models that could potentially be used for modeling bacterial pollutants in agricultural watersheds have been assessed in this study. No one model suits all modeling criteria. Pathogen predictions have proved variable and no model was capable of accounting for all geological and hydrological factors in addition to modeling the physical transport of bacteria in surface runoff. This assessment summarizes commonly used models and their capacity to model water pollution while also providing a good reference point for the microbial risk assessment of waterborne pathogens.