This special issue of Environmental Science and Policy presents the outcomes of the WETwin project (enhancing the role of wetlands in integrated water resources management for twinned river basins in EU, Africa and South-America in support of EU Water Initiatives), an international research project funded by the FP7 programme of the European Commission. The project aimed to improve wetland management by maximising benefits from wetland use while maintaining ecological health, using case studies from Europe, Africa and South America. In much of the less developed world, data on wetland functions, processes and values are scarce even while wetlands often provide a critical component of livelihoods. Management decisions on balancing competing demands for wetland use must often be made in the absence of comprehensive information. This paper introduces the approach developed and tested under WETwin to evaluate wetland management structures and solutions in data-poor contexts, summarising a conceptual framework which has evolved from seven very diverse case studies. A structured, modular approach was devised which combined multi-criteria analysis, trade-off analysis and vulnerability analysis, drawing on best available information, including quantitative modelling, qualitative “expert opinion”, and local stakeholders' knowledge and values. The approach used in WETwin has three important strengths: it involves stakeholders at all stages of the decision process, it combines qualitative and quantitative data (and therefore allows inclusion of poorly known and potentially important system components) and finally, it provides a relatively simple and structured approach to evaluate wetland management interventions and integrate impact, feasibility and institutional assessments, vulnerability analysis and trade-off analysis. The overall conceptual framework developed for WETwin was found to be robust and transferable to different contexts.