The Mesta-Nestos river basin in Bulgaria and Greece is a case study for transboundary decision-making support in south-eastern Europe and a show-case for the development of methodologies and information-gathering for the integrated regional planning of water resources. Land-use conflicts in this water-scarce region cover a wide spectrum of activities like agricultural irrigation, drinking water production, diversions for industrial water, and risk of pollution from mining, to name a few examples.Measurements of the water quality were carried out in the upper basin. Results will be illustrated by the example of the environmental situation in the alpine region of the Pirin National Park as well as in the Razlog Basin with a stronger anthropogenic impact and pollution around a former uranium mine near the village of Ele(s)nica. The social and economic development of this transboundary region is a recently established priority for the future. It will mean an increase in water usage and more stress for the water resources if regional impacts of global climate change are verified. Problem-focused management of the catchment area as a whole on the basis of proved geo-data sets is needed for the future.