Limited information exists on the modelling of Cryptosporidium in water catchments. This lack of data underlines the uncertainty that surrounds the catchment modelling of Cryptosporidium, the variability observed in model predictions, and the need to expand research in modelling this parasite. The objective was to examine and evaluate the use of the Soil and Water Assessment Tool (SWAT) to simulate Cryptosporidium populations for water catchments. The Fergus catchment in the west of Ireland was the focus of SWAT model development because it has been susceptible to Cryptosporidium contamination of raw water. Flow calibration was carried out from February 2003 until February 2005 [Coefficient of determination (R(2)) = 0.83, Nash-Sutcliffe efficiency (E) = 0.78]. Cryptosporidium simulations were run using data from January 2004 until December 2006. Initial results indicated that the model can be used to predict oocyst concentrations in water catchments. Mean monthly prediction ranged from 4.8 oocysts l(-1) to 0.004 oocysts l(-1) (mean = 0.9 oocysts l(-1)). Predictions highlight late autumn/winter and early spring as being the highest risk periods. Manure application was identified as being a significant source of the pathogen to which management strategies could be focussed to reduce potential levels of Cryptosporidium in catchment waters. Further model development, using observed oocyst levels, is needed to quantitatively assess model accuracy. Overall, the study contributes to new knowledge in pathogen transport using SWAT and represents a first step in developing a catchment model capable of predicting potential human exposure to Cryptosporidium. (C) 2010 IAgrE. Published by Elsevier Ltd. All rights reserved.