The Transboundary Freshwater Dispute Database provides a framework for quantitative, global-scale explorations of the relationship between freshwater resources and international cooperation and conflict. Projects were designed to test common theories linking freshwater resources to cooperation and conflict, in particular within the context of geography and environmental security. The projects, which follow in sequence, consider three main hypotheses on the likelihood and intensity of water resource disputes. To test these hypotheses, a unique set of tools was created that links water-specific event data with a geographic information system (GIS) that meshes biophysical, political, and socioeconomic data sets at the river basin and other scales. There are three linked data sets: (1) an event data set documenting historical water relations, including a methodology for identifying and classifying events by their intensity of cooperation/conflict; (2) a GIS data set of countries and international basins, both current and historical; and (3) a spatial data set of biophysical, socioeconomic, and political variables, linked to the GIS. This paper describes the hypotheses, the above tools created to test them, and a methodological framework for utilizing the linked event and GIS data sets, providing three projects as examples: (1) indicators of international basins at risk of political tensions, (2) relationships between internal and international hydropolitics in three geographic regions, and (3) hydroclimatological variables and international water relations.