The accelerating pace of climate change mainly on the adjacent territory of the Danube basin, contribute to the essential eutrophication of water basins within the region. The results indicate that air temperature recorded a double warming compared to territories from the central part of the country. On the background the accelerated warming there is a declining trend and of annual rainfall amounts. These climate changes, especially in recent decades have led to significant increase of water temperature in rivers and lakes. Thus, it constituted in the years 1990-2000 by 0.7 and 1.50C compared to the period 1980-1990, and by 1.0...2,00C accordingly in the years 2000-2013 compared to the previous decade. The significant increase of temperature during the last decade contributed to the intensification of algae growth and together with other factors contributed to the increase by about 20% of the nitrogen content, thus ensuring the ―flowering‖ with 50% of the water bodies’ volume.