The Republic of Moldova is situated among countries with relatively poor water resources, therefore their protection and rational use remains a national problem. Due to its geographic position, the Republic of Moldova is subjected to transboundary pollution. The current work represents the estimation of the buffering capacity on the Dniester River waters and its tributaries between November 2008 and October 2009. Decrease of the buffering capacity in water basins leads to disruption of the normal activity of aquatic biota, by increasing the toxicity in their living environment. On the basis of the results of measurements, suggestions for the improvement of the situation will be made and for enhancing public awareness and public authorities involvement.