Storm-induced Escherichia coli pulses in the Motueka River (2074 km 2 ) and the Sherry River (78.4 km 2 ) are modelled. The model focuses on the catchment outlets, representing key processes, including E. coli transfer to and from the river bed, with account taken of the hysteresis in, and non-linear, non-stationary, response of E. coli concentrations to river stormflows. The model fits the Motueka River observations well, but less well in the Sherry River. A greatly simplified description of headwater and riparian inputs is satisfactory at the larger catchment scale where near-field, in-channel processes dominate the response. Spatial heterogeneity in rainfall-run-off and faecal sources probably contribute to the poorer fit in the smaller catchment. Despite using a relatively small number of driving variables and parameters, the model has the potential to predict real-time E. coli input to Tasman Bay in river plumes causing shellfish and bathing beach contamination.