ABSTRACT A model of Escherichia coli concentrations in the runoff from grazed pastures was developed to increase our knowledge and ability to predict the relative impact of both cow and sheep grazing on water quality. Input parameters to the initial model were derived from published data and model outputs were compared with measured E. coli runoff concentration data from both sheep and cow grazed pasture. The model was designed to represent the complexities of year-round rotational grazing farm system. For cow grazing, the model estimated runoff E. coli concentrations in the same order of magnitude as the measured data. However, for sheep grazing, the model underestimated the measured runoff E. coli concentrations by 1.5 orders of magnitude. To understand this negative result, Monte Carlo simulation techniques were used to conduct a sensitivity analysis of the input parameters. This analysis identified that runoff concentrations were highly sensitive to inputs of the E. coli concentrations in the dung and the mobilisation rates of E. coli from the dung. This modelling study demonstrates that significant gaps and uncertainties remain in our understanding and prediction of the mobilisation and transport of E. coli from grazed pasture systems. HIGHLIGHTS Faecal microbial losses from agriculture are poorly understood. A runoff concentration model was developed based on the area of faecal pats. The area-based model appears to work for cow grazed pastures. The area-based model does not work for sheep grazed pastures.