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Scientific research suggests that the impact of pathogens, such as verotoxigenic (VTEC) Escherichia coli and Cryptosporidium, may be intensified by the potential effects of climate change. It is predicted that extremes of the hydrological cycle will accompany global warming and both are likely to affect the nature of pathogens in the environment and their fate and transport. Regulations, such as the EU Water Framework Directive and the US Clean Water Act, highlight the need for models capable of predicting fecal pathogen fluctuations from watersheds with varying land uses. Previous research work on the applicability of watershed models to simulate daily pathogen concentrations has indicated that sufficient capabilities exist to model pathogen transport; however, additional research is required to account for future climate variability and identify risk scenarios. Integration of watershed-pathogen modeling capabilities with climate change predictions can enable investigation into the potential impacts on pathogenic organisms. To date legislation's, such as the Clean Water Act in the USA and the Water Framework Directive in Europe, have failed to take direct account of the risks posed by climate change. The objective of this study is to examine potential climate change impacts on pathogens and assess the use of watershed-pathogen modeling applications to prepare for future scenarios. Deriving relevant scenarios and simulation of these through watershed modeling applications can provide the basis to develop appropriate remediation measures in preparation for climate impacts on waterborne microorganisms.