Devising policy instruments and interventions that can manage and mitigate the risks associated with microbial watercourse pollution is a significant concern of the contemporary environmental protection agenda. This paper reports on the work of a citizens’ jury that sought to elicit reasoned public judgments about the nature and acceptability of these risks as they relate to the role of livestock farming, and what might constitute socially acceptable and sustainable pathways to their management. By exploring this issue through a logical and sequential process of risk characterisation, risk assessment and risk management, the paper reveals how citizens’ juries can be used to contextualise and structure science-policy apprehensions of microbial watercourse pollution, and highlight where priorities for innovation and intervention might lie. Reactions and responses of participants to the jury process and its outputs, including issues of social and practical impact of the exercise, are also considered. The jury technique is argued to be useful in the way it cuts across disparate domains of responsibility and expertise for the governance of environmental risks, and therein challenges decision makers to think more broadly about the political, moral and economic framings of otherwise narrowly conceived science-policy problems.