ENAs Lithuania seeks to integrate into the European Union, much more attention will have to be paid to the environment protection. Improvement of water quality is the most difficult task and it demands the biggest financial supply. Till now the bulk of attention has been paid to the diminishing of point sources of pollution. Water protection policy executed in Lithuania could be called actions aimed at binding sewage in the sewage treatment plants as much as possible. The results of such a policy were not satisfactory, because only one element of the complex natural water system was controlled. If we want to save and improve the state of Lithuanian water resources, it is necessary to govern the entire water system, all sources of pollution and all processes determining water quality. It can be done only if the situation is examined broadly and watershed management projects are made. When the present Lithuanian position and possibilities were evaluated, it was ascertained that the underlying strategic goal of water protection should be conservation of both underground water and clean surface waters. The most important task is to control point and nonpoint sources of pollution in rural areas. One of the most effective and realizable means for protection of diffusive sources is the enlargement of woodlands and creation of structures with good indices of surface runoff regulation. Thus it is necessary to coordinate watershed management projects with the documents of territory planning.Besides, problems of water resources should be integrated into such programs as agriculture development, shake-up of the countryside, territory usage management and so on. For the efficiency of the water management policy, it is suggested to separate the strategic and the operative levels. For that purpose Lithuanian water monitoring should be matched with the strategic plans and watershed management projects.