Ecosystem services that sustain human wellbeing depend on the continued functioning of ecosystems, proper management and supporting institutions. However, the interaction between these factors and ecosystem services is poorly understood. Therefore, we assessed how ecosystem services are represented in policy measures, recognized by local population and affected by weather extremes. We studied the Hungarian and Romanian parts of the flood-exposed Tisza River Basin, where all these factors are relevant for regional land and water management. Our qualitative assessment shows that, although the two regions share similar environmental conditions, the different social and institutional settings of the two countries cause a divergence in ecosystem services. Locally produced provisioning services are better recognized in Romania, while regulating (particularly water-regulation) and cultural services are better recognized in Hungary. Food supply is most affected by climate-related weather extremes and most strongly controlled by policy measures in both countries. However, especially in Romania, policy measures support medicinal and genetic resources, and some regulating (e.g. pest regulation) and cultural services, only weakly or indirectly. We conclude that the analysis of ecosystem services in relation to climate-related weather extremes, policy measures and people's recognition can contribute to a better management of the Tisza River Basin. We suggest that a better incorporation of ecosystem services in policy and management strategies could enhance and diversify the ecosystem service supply. A further quantification of ecosystem services can, therefore, provide a base for targeted and integrated planning and improved regional policy making.