There is increasing recognition of the adverse impacts of agricultural practices on microbial water quality leading to increased expectation on farmers to manage environmental impacts on water quality. Therefore, farmers require a tool to help them prioritise mitigations targeted at reducing faecal contamination of surface water. A farm-scale risk index was developed from modelled data on the predicted losses of E. coli from selected farm practices. The farm-scale data was then converted to a catchment scale risk value and calibrated against stream E. coli concentration data measured in five catchments. The data from the 5 catchments indicates that there is a relationship between the risk of E. coli losses from some farm practices and the resulting E. coli levels in the streams. The results show that the adoption of existing mitigation options for faecal contamination should result in a substantial reduction of E. coli concentrations in streams flowing through catchments used for intensive dairy farming. However, the relatively high E. coli concentrations in the stream when the calculated risk index values are low indicate that currently available mitigation practices may not be sufficient to achieve contact recreational water quality standards in many catchments due to other sources of E. coli. This risk-index approach can be incorporated into existing decision support tools to enable farmers to manage faecal contamination impacts from their farming operations.