WETwin is a research project supported by the European Commission under the Seventh Framework Program. Its overall objective is to enhance the role of wetlands in basin-scale Integrated Water Resources Management (IWRM), with the aim of improving the community service functions while conserving good ecological status. This report aims to be a guideline supporting the integrated and adaptive management of wetlands. This guideline is embedded into a Conceptual Framework, which is introduced in Chapter 2. Further, the guideline consists of two main parts: Vulnerability Assessment (VA) in Chapter 3, and Multi-Criteria decision Analysis (MCA) in Chapter 4. The descriptions of these methodologies are illustrated by examples from the WETwin case studies. Also, references have been incorporated into the texts with regard to relevant publications and to other WETwin project reports. In this way, the guideline covers all relevant outcomes and results of WETwin, and it also works as a meta-document for the most important deliverables of the project. Chapter 5 at the end of the report draws conclusions and gives recommendations for the joint use of VA and MCA. The targeted users of this guideline are professionals, who are in charge of elaborating wetland management plans.