Water availability and environmental protection are critical aspects of sustainable development, particularly in regions such as the Mediterranean, characterized by diverse landscapes and variable climatic conditions. The research described in this communication aims to assess the effect of the environmental flow policy on the availability of water for Mediterranean basins. We used runoff estimations for the Mediterranean taken from two global hydrological models, H08 and CWatM, included in the Inter-Sectoral Impact Model Intercomparison Project ISIMIP3b output datasets (Warszawski et al., Proceedings of the National Academy of Sciences 111:3228–3232, 2014). Runoff data was processed using a water resource management model based on GIS to obtain potential water availability in Mediterranean basins. The reservoir data was obtained combining three databases: ICOLD-WRD, GRanD, and GOODD. Potential water availability refers to the highest possible demand that can be met at a specific location in a river network. This is achieved by utilizing the available reservoir storage to regulate flow, while adhering to practical management practices, maintaining environmental flow requirements, and meeting established reliability standards. The WAAPA model was run without ecological flow and with several alternative ecological flow allocations, following different methods of estimation. The results showed that the allocation of environmental flow can reduce total water availability in the Mediterranean between 40 and 60%, depending on the hypothesis adopted. If individual basins are considered, this range is significantly wider. Basins with a large storage volume compared to the mean annual flow show a comparatively lower sensitivity to environmental flow allocation. This study provides insight for policy makers and stakeholders, enabling them to make informed decisions about environmental flow allocation considering its impact on water availability.