Prut river basin has a predominantly agricultural and water resources are vital to the human settlements and the regional economy. Climate change and irrational use of water resources significantly affect water supply and ecosystem components of this river basin. Because superficial knowledge of the current state of water resources, the measures taken by the authorities are not effective, and economic and environmental problems are getting worse. The main research objectives of this study are following: assessment of water captured and used by sources and domains of use; analysis of water losses; establishing trends and limits of captured and used waters; identification of problematic situations existing of water use in the Prut river basin; elaborating of recommendations to optimize the use and state of water; creating informational and methodological support necessary for development the Plan Measures on the Prut River Basin.