Monitoring water quality in drinking water distribution systems is the base for pro-active approaches to prevent or manage emerging water quality issues, and such a monitoring requires a strategic selection of relevant and representative monitoring sites. GISMOWA is a new GIS and risk-based analysis tool to identify and to prioritise pipe segments for water quality monitoring and to comply with existing monitoring and sampling guidelines. The tool was designed to integrate multiple parameters categorized as 1) Hydraulic and structural weaknesses in the system, e.g. residence time, 2) External threats, e.g. contaminated sites, and 3) Sensitive consumers, e.g. hospitals in a GIS environment. The tool used a multi-criteria decision analysis to evaluate multiple monitoring site parameters and map zones particularly suitable for water quality monitoring. GISMOWA was applied to Danish water distribution systems as a transparent and simple-to-use tool which facilitated a complete overview of the distribution system, including sensitive consumers and consumers in general, and thus fulfilling a precondition for a HACCP-based monitoring strategy of drinking water.