In the E.U. following the old 5th Environmental Action Program (EAP) of 1994 and the new 6th EAP for the sustainable development in 2001, we confront the strategic management problem of aquatic resources at the regional and watershed level. What should be the goals for a new strategic management of natural and aquatic resources in a Region of Greece such as Thessaly? The present paper is concerned with the protection, prevention and strategic environmental planning of aquatic resources and water purification in the Thessaly basin as well as the protection of these resources from the pollution and depletion, which might result from various national water resource programs and plans which are already in operation. The aforementioned aim is a product of research on the goals, actions and proposals, which depict the problem of aquatic resource management related to pollution, the link with agricultural activities and the overall problem of water. Primarily, a general profile of the water situation and problems is presented for the Thessaly basin, including water pollution and the problems related to the rational management and protection of aquatic resources. Also, the prevention of natural water-involved disasters is explored which in turn points to the need for a new strategic scheme for environmental management of aquatic resources and purification and to the institution of new water policy actions and measures for the Thessaly basin in central Greece. (C) 2009 Elsevier B.V. All rights reserved.