From 12 to 22 of September 2013 it was organized and performed a comprehensive ecological expedition on the Prut River, within the borders of the Republic of Moldova. It is a part of International Danube Expedition “JDS-3”, organized by the Commission for the Protection of the Danube River in the period from 12 August to 26 of September in the Danube basin. The main objective of the expedition focused on comprehensive ecological assessment of the basin of the Prut River within the borders of the Republic of Moldova. Expedition program included sampling both the Prut River, and the mouth of its tributaries, identification of pollution sources and risks to ecosystem, highlighting the most polluted areas, etc. Environmental parameters were evaluated in accordance with the EU Water Framework Directive, which started to be implemented gradually in the Republic of Moldova. Also, expedition offered an opportunity to assess the involvement of local authorities and population in solving environmental issues from the basin of Prut, in order to take measures to increase their awareness on the need for protection and rational use of water resources. The essence of this assessment was based in particular on sampling of water and sediments throughout the river segment, also on analyses and intercomparison of the samples regarding new hazardous substances and assessed the ecological state of the river, according to the Water Framework Directive, detection of sources of wastewater and sewage discharged into the river, highlighting the most polluted parts of the river with the specification of the causes, consequences and mitigation measures, complex chemical analysis in the laboratory with the specification of the most polluted sectors and existing overriding pollutants, identification of damages caused by wastewater, highlighting existing pollution sources and conducted complex investigations in terms hydrographic, hydrological, geomorphological, landscape, hydrochemical, hydrobiological, etc. After finishing complex expedition,,PRUT 2013” and analysis of data obtained during the studies and investigations conducted by representatives of the participating institutions were highlighted a number of important conclusions, which are reflected in the article.