Ostrom’s framework to analyse the sustainability of social-ecological systems has attracted great interest in the last years. It was not conceived to characterise systems, but its nature and structure make it very appealing to be used with this objective. However, its use to characterise three social-ecological systems where common-pool resource management is central created some methodological struggles and difficulties for comparing outcomes. This paper aims to present some adaptations developed for improving the framework’s comprehensiveness and practical applicability at local level, such as a transdisciplinary description of the second-level variables, the definition of a set of third-level variables to facilitate and enrich the descriptions and additional guidelines for gathering the information and planning data searching processes at local level. The whole process of adapting and applying the framework was the result of collaboration among scientists, and local researchers and stakeholders. The adapted framework permitted a comprehensive and comparable characterisation of the social-ecological systems analysed and facilitated its use by the local communities.