Urban water systems involve complex interactions between ecological, social and economic factors. Integrated management approaches are needed to achieve multiple policy objectives in the sector and can be pursued at a range of spatial scales. Small-scale integrated water projects are both feasible and valuable in dynamic urban environments in developing countries. This paper develops a method for the prioritization of localities for integrated projects and applies this to the city of Jakarta. A set of indicators is defined following a systems approach, populated, displayed through a dashboard and mapped, and the relationships between indicators are analysed. Indicator-based prioritization allows policy-makers to guide resources to integrated projects to contribute effectively to the achievement of policy goals.