This report presents results of the studies conducted in 2002 of eukaryotic algae and cyanobacteria found in the River Dunajec in the area of the newly built dam reservoirs in Czorsztyn and Sromowce. The studies demonstrated that diatoms were the dominant group in both the river (at 74 %) and the dam reservoirs (at 32 %), and that among the diatoms collected, eutraphenthic [van Dam et al. 1994] species usually prevailed. The diatom group, characterized by a broad ecological scale (tolerant), predominated slightly only at Station 3 located downstream from the dam reservoirs. This variation, which was probably connected with improved water quality in this part of the river, was the result of the sedimentation of pollutants in the dam reservoirs. Equally unexpected was the mass development of Didymosphenia geminata in this area. It occupied not only spots in the riverbed of the River Dunajec, but it also spread to the riversides and even to the river arms close to the confluence of the streams flowing from the Pieniny Mountains. The quantitatively dominant species in this area was Cladophora glomerata, which is an excellent habitat for other algae, particularly diatoms. The ultrastructure of its cell and cell wall is of great significance since it reflects the environmental conditions in which it lives. The ultrastructure of the Cladophora glomerata that occurred at different stations did not differ significantly, nor did it indicate the existence of any considerable hazard resulting from environmental pollution.