This article deals with the topical issue of international environmental cooperation in the field of water resources protection in the Baltic region. As of the beginning of the XXI century it was possible to observe the negative trend that was developing in the waters of the Baltic Sea and posing a threat to the whole hydrosphere of the region. In the course of the study it was stressed that due to the border neighborhood and the unity of the adjacent water area, international cooperation for many years was built between nine major states: Russia, Finland, Sweden, Estonia, Denmark, Latvia, Poland, Lithuania and Germany. The experience of cooperation between Russia and Germany in the Baltic territories was particularly emphasized. Also, it was revealed that the use of the waters of the Baltic Sea affected the interests of Norway, Ukraine, Belarus, the Czech Republic, and Slovakia. The article mentions the history of the formation of international regulation and legal acts aimed at protecting the security of the Baltic Sea. The main ecological problems of inland waters of the Baltic Sea are considered, the possible ways of their solution are indicated. As the most dangerous problems of the Baltic Sea, chemical changes in the composition of sea water and the accumulation of harmful elements in it due to industrial emissions, municipal waste, the burial of shells and chemical munitions, and sunken ships were mentioned. The researchers have studied in detail the development of the legislative framework and international acts in the field of nature protection related to inland waters. The study noted a number of measures of interstate cooperation with major environmental organizations, the early application of which in the Baltic Sea by countries whose territories are part of the region will minimize the consequences of damage already inflicted on the biosphere. Possible preventive measures were indicated to stabilize and restore the normal hydroecological situation. The authors noted that the study of this issue could positively influence the creation of experience in organizing international environmental activities not only in the Baltic area, but also in relation to all major inland water sources of the planet.