This paper addresses the issue of the risk that livestock agriculture has for human exposure to pathogenic organisms from watercourses (including bathing waters or consumption of contaminated shellfish). The paper describes trends in livestock farming, the extent of microbial contamination of water, and what farmers can do to reduce transfers. A case is made for interdisciplinary and stakeholder approaches to assessing the risk of potential pathogen transfers. Conceptually, this requires integrating fixed social risk factors with fixed physical risk factors. Recognition of the uncertainties in the evidence base presents a challenge in communicating risk. But participatory approaches offer an opportunity to build consensus around potential programmes of action through deliberation by key stakeholder groups.