The amount of industrial waste released into the Morava River has decreased substantially since the late 1950s. This has led to a marked increase in phytoplankton abundance and species diversity. In the past, the Dyje River, a main right-side tributary of the Morava, served as a major source of planktonic algae for the lowermost stretch of the Morava River. At present, production and biological processes in the Nove Mlyny reservoirs significantly influence water quality. The quantity of phytoplankton has decreased but during hot summer periods the floating biomass of bloom forming Cyanophyta has increased significantly. The increase of colonial cyanophytes is an undesirable incidental phenomenon associated with the improvement of water quality in terms of allochthonous organic pollution. This was also promoted by the damming of the Dyje River in its lower floodplain area some fifteen years ago. Observations from 2002 indicate that a bloom of cyanophytes could soon also affect the middle stretch of the Morava. The lower stretch of the Morava supports a species-rich community of planktonic algae and diatoms, but above all, green flagellated and coccal algae. The Morava represents an important source of algal inoculums for the Danube and it contributes to the species diversity at the point where it enters the Pannonian Lowland. In this stretch of the river 25 genera with 58 species of cyanophytes and 181 genera with 634 species and infraspecific taxa of different groups of algae have been identified. Phytoplankton abundance has increased several times in comparison to the late 1950s. The highest values measured in 2002 were close to 100,000 cells per ml, and the chlorophyll?alpha concentration was 100 mug/l.