In order to effectively manage the wide variety of physical, chemical biological and ecological processes in a sensitive coastal environment such as the Black Sea, current environmental management objectives are no longer sufficient: a new management approach has to address the intimate functional linkage between the river basin and the costal environment. Current water quality legislation requires compliance to emission levels based on the chemical analysis of water samples taken at discharge points, such as treatment plants discharging into rivers. While such measures provide a relative indication of the water quality at the point of discharge, they fail to describe accurately and sufficiently the quality of the water received from the watershed or basin. As water flows through the catchment, rainfall run-off from urban and agricultural areas carries sediments, pesticides, and other chemicals into river systems, which lead to coastal waters. The impact of the Kosovo crisis on the Danube ecosystems provides a poignant example of the effects of such diffused pollution mechanisms and reveals a number of interesting pollution mechanisms. This paper discusses both the effects of diffused pollution on the Black Sea, drawing from state-of-the-art reports on the Danube, and proposes a framework for a decision support system based on distributed hydrological and pollution transport simulation models and GIS. The use of ecological health indicators and fuzzy inference supporting decisions on regional planning within this framework is also advocated. It is also argued that even the recently produced GEF document on Black Sea protection scenarios should benefit significantly if the concept of pollution reduction from both urban, industrial and rural areas should undergo a systematic conceptual update in the view of the recent recommendations of the UNEP IETC (2000) document.