Parallel policy developments driven in the USA by the Clean Water Act and in Europe by the Water Framework Directive have focused attention on the need for quantitative information on the fluxes of faecal indicator bacteria in catchment systems. Data are required on point and diffuse source loadings, fate and transport of these non-conservative parameters, on the land surface, within soil systems, in groundwater, streams, impoundments and nearshore waters. This new information is needed by regulators to inform Total Maximum Daily Load estimates in the USA and Programmes of Measures in Europe both designed to prevent impairment of water quality at locations where compliance is assessed against health-based standards for drinking, bathing or shellfish harvesting. In the UK, the majority of catchment-scale activity in this field has been undertaken by physical geographers although microbial flux analysis and modelling has received much less attention from the research and policy communities than, for example, the nutrient parameters. This paper charts the policy drivers now operative and assesses the evidence base to support current policy questions. Finally, gaps and priority research questions are identified.