Abstract Enabling knowledge exchange between scientists and decision-makers is becoming increasingly necessary to promote the development of effective decision-support tools (DSTs) for environmental management. Participation of stakeholders in the design process beyond a basic level of consultation is essential for promoting trust in modelled outputs and accelerating eventual uptake of resulting tools and models by end-user communities. This study outlines the development of a DST to visualise and communicate the spatial and temporal patterns of E. coli (a faecal indicator organism) on agricultural land, as a first step in managing microbial pollution risks to the wider environment. A participatory approach was used to engage regulators, catchment managers, environmental scientists, farmers and farm advisors, researchers in geospatial technologies and water industry staff in the co-design of a novel, user-friendly and accessible DST for guiding on-farm microbial risk assessment. Recommendations for maximising the benefits of a participatory process to DST design are discussed with reference to a series of opportunities and limitations identified by our stakeholder cohort during the development of the Visualising Pathogen & Environmental Risk (ViPER) DST. The resulting toolkit provides environmental managers and farm advisors with one of the first freely-available DSTs for visualising patterns of E. coli inputs to pasture in space and time, and begins to address the lack of advisory tools currently available for informing decision-making with respect to managing microbial risks in agricultural systems.