SWAT (Soil and Water Assessment Tool) represents a dynamic catchment modelling application that can be applied to any river basin and used to quantify the impact of land management practices on water quality over a continuous period. The objective of this study is to apply the Soil and Water Assessment Tool (SWAT) to model pathogen transport, simulate management practices affecting water quality and predict pathogen loads in Irish catchments. Based on input data regarding agricultural practice, demographics and hydrological parameters for the river Fergus catchment, SWAT was run to predict concentrations of Escherichia coli. Hydrometric validation results display a very good linear relationship between observed and predicted data (Coefficient of determination R-2 = 0.83, Nash-Sutcliffe efficiency E = 0.78) and indicate satisfactory simulation of hydrologic processes within the catchment. To date, pathogen predictions have proved variable between observed and simulated figures. Based on recommended values for the quantification of catchment modelling accuracy, predictions for E. coli can be described as acceptable and satisfactory with R-2 = 0.68 and E = 0.59. Extensive monitoring is required for such simulations and the current study represents partial validation. Results suggest that although the capabilities exist to simulate pathogen transport in catchments, the capacity to accurately account for all factors that can contribute to water degradation is uncertain. The sensitivity analysis identified the bacteria partition coefficient (BACTKDDB) as the most important input parameter. In addition it reveals areas where further research is required, particularly in assessing the initial concentration of E. coli in human/animal waste. The developed model provides a tool capable of protecting water sources and human health from waterborne pathogens. (C) 2009 Elsevier B.V. All rights reserved.