GOWARE (transnational Guide toward an Optimal WAter REgime) represents a Decision Support Tool (DST) developed to support the implementation of innovative Best Management Practices (BMPs) for drinking water protection and flood/drought risk mitigation. The tool is one of the main outputs of the PROLINE-CE Project, an EU project funded within the Interreg Central Europe (CE) Programme (2014-2020). The aim of this paper is illustrating the design and the methodological approaches proposed for the operative development of the tool. Furthermore, the paper provides the results of a number of tests carried out to evaluate the understandability of the analysis processes and assessing the stakeholders acceptance. Specifically, GOWARE-DST has been developed for supporting single users or groups of users in the decision-making process. The tool has been provided with a catalogue of 92 BMPs to handle water issues in different land use contexts. The selection of practices suitable for addressing the specific users requirements is supported by the Analytic Hierarchy Process, a method that allows filtering a subset of BMPs by accounting for the relative importance that the user assigns to each characterizing criterion. GOWARE-DST represents an innovative tool for supporting users at different levels of planning (operational and strategic) by promoting sustainable land and water management and defining long-term governance activities.