Management of trans-boundary river basins is a major issue that has attracted great attention in recent years. The European Water Framework Directive (WFD) recommends management at a river basin level, overlooking any national or administrative borders. This new managerial approach impels water managers to disregard the trans-boundary nature of the water resources while considering an integrated river basin where only geographical boundaries exist.

The new challenge for scientists and water managers is the establishment of water agreements between countries sharing water resources. These agreements should aim at the settlement of tensions and conflicts while providing the essential framework for cooperation and consensus building. Apparently, the content of these agreements should comply with international law and the relevant international conventions especially, as noted by the WFD, the UNECE Convention on the Protection and Use of Trans-boundary Watercourses and International Lakes (known as the Helsinki Rules), approved by the European Council in 1995.

This paper examines the efficiency of water agreements and their precedent negotiations using the best known international examples while focusing on the Greek–Bulgarian agreement for the waters of the Nestos/Mesta River and its compliance with the WFD and the Helsinki Rules. As shown, the two countries have failed to implement a joint effort to put it into action; hence a methodological framework is proposed including certain strategic steps that can guide the two countries to a more effective and applicable water agreement taking into account the peculiarities of this trans-boundary area.

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