Recent major political changes in Central and Eastern Europe opened new avenues for environmental and water quality management. In the past there was practically no need for the application of systems analysis or any policy-related sciences. As an exceptional case the eutrophication control of Lake Balaton (Hungary) is discussed. The counterpart example is the Gabcikovo-Nagymaros barrage complex (Danube): here a systematic assessment is missing even today. The type of the analysis which would be required is illustrated by two examples: eutrophication of the upstream reservoir of the complex and oxygen household of pne of the side arms of the Danube. Future applications of systems analysis depend primarily on desired institutional changes and environmental legislation, as due to past economic development paths large number of problems exist in Central and Eastern Europe. These are discussed primarily for Hungary. Skill and scientific knowledge exist but experiences in application are lacking. Environmental education should be modernized. A specialized technology transfer is needed also towards changes of institutional structures and legislation, and also the training of managers. The most important task under the existing economic pressure is the preparation of well tailored, cost-effective water pollution control strategies for countries in question. This requires in itself a systems analytical approach.

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