National borders remain an impediment to efficient preservation of biodiversity and ecosystems. For transboundary water resources, conservation planning becomes more challenging, as competitive interests make these sensitive and productive systems focal points of interstate conflicts.

This global study aims to explore the patterns of protection coverage for transnational lakes and their catchments, highlighting gaps and inconsistencies at the protection observed among countries sharing the same lake.

Identifying 793 transnational lakes globally, we initially investigated protection coverage at their water bodies. Next, we explored protection coverage patterns across each lake’s catchment, in which we also quantified human pressures’ extent and intensity. Socio-economic and political parameters were examined as potential predictors of the observed patterns.

Only half of the world’s transnational lakes are fully or partly covered by existing protected areas. Our analysis demonstrated that in only 37% of the protected transnational lakes, the extent of protection coverage was similar in the neighboring counties sharing the same lake. Protection patterns were not driven by the relative area of the transnational lakes found in the neighboring countries. Moreover, protection cover focuses mainly on lakes’ water surface ignoring the terrestrial surroundings, while more than 75% of the catchments are subjected to intense human pressures.

Providing the first overview of the protection gaps of transnational lakes globally, we highlight a failure of policy responses to cross-border conservation of sensitive freshwater ecosystems. Consequently, such limitations are likely to loom risks for human well‐being and for the initiation of intense conflicts.