Coordination on the management of transboundary waters is crucial for the development of riparian regions; nevertheless, lack of common legislation frameworks and communication channels jeopardize any cooperation among transboundary parties. The paper investigates the progress that has been conducted before and after the implementation of European Union’s common water policies in the management of transboundary surface waters and groundwaters shared between Bulgaria and Greece. To do so, the latest derivatives of the Water Framework and Flood Directives’ implementation process in both countries are analysed and processed to identify the quality and quantity (floods) of the surface waters’ status on the three transboundary river basins’ which are shared between the two countries, as well as the quality status of the groundwater bodies located in the boundary area. The outputs are compared with identified problems and pressures that were reported in the transboundary area before the operational implementation of the Directives. In terms of surface waters, the research demonstrates a remarkable amelioration of the inflows’ quality status to the downstream river basins. The most significant problem is induced floods due to transboundary waters, however the recent activation of a cooperation mechanism is a very promising engagement. Finally, it has been established that the transboundary groundwater bodies are of good status, but additional groundwater formations are proposed to be designated as transboundary ones. Concluding, legislative and technical aspects of the EU water Directives have significantly fostered shared waters management in the case study area, with the proposed methodological framework to be applicable in all EU’s shared waters.