Source water protection planning (SWPP) is an approach to prevent contamination of ground and surface water in watersheds where these resources may be abstracted for drinking or used for recreation. For SWPP the hazards within a watershed that could contribute to water contamination are identified together with the pathways that link them to the water resource. In rural areas, farms are significant potential sources of pathogens. A risk-based index can be used to support the assessment of the potential for contamination following guidelines on safety and operational efficacy of processes and practices developed as beneficial approaches to agricultural land management. Evaluation of the health risk for a target population requires knowledge of the strength of the hazard with respect to the pathogen load (mass concentration). Manure handling and on-site wastewater treatment systems form the most important hazards, and both can comprise confined and unconfined source elements. There is also a need to understand the modification of pathogen numbers (attenuation) together with characteristics of the established pathways (surface or subsurface), which allow the movement of the contaminant species from a source to a receptor (water source). Many practices for manure management have not been fully evaluated for their impact on pathogen survival and transport in the environment. A key component is the identification of potential pathways of contaminant transport. This requires the development of a suitable digital elevation model of the watershed for surface movement and information on local groundwater aquifer systems for subsurface flows. Both require detailed soils and geological information. The pathways to surface and groundwater resources can then be identified. Details of land management, farm management practices(including animal and manure management) and agronomic practices have to be obtained, possibly from questionnaires completed by each producer within the watershed. To confirm that potential pathways are active requires some microbial source tracking. One possibility is to identify the molecular types of Escherichia coli present in each hazard on a farm. An essential part of any such index is the identification of mitigation strategies and practices that can reduce the magnitude of the hazard or block open pathways.