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 presents the results of the analysis of the institutional capacity to implement IWRM and existing guidelines in selected case study sites of the WETwin project (Gemenc (Hungary), Ga-Mampa (South Africa), Nabajjuzi and Namatala (Uganda)). It includes: i) a presentation of the conceptual approach used to analyze institutional capacity in case studies, in particular, the main concepts and definitions of institutional capacity and its links to performance of the wetland management institutions; ii) a description of the methodology used for the analysis of four case studies; iii) the detailed assessment of the components of institutional capacity using the cross-case comparison method, as well as a discussion of the major findings of the application of the methodology in the case studies; and iv) a summary of all the lessons learnt during this exercise and recommendations for improvements of the institutional capacity in the case study areas and in wetland management in general.