To understand the potential impact of the Three Gorges Reservoir on the aquatic ecosystem after the damming of the Yangtze River, we studied the community composition and temporal abundance distribution of algae in two types of water bodies:a segment of the Jialing River near its confluence with the Yangtze River as an example of the river-lake type, and Shuanglong Lake in Chongqing as an example of the lake type. In total, 107 species belonging to 58 genera of 7 phyla were identified in the study area of the Jialing River, dominated by three groups with 49.5% diatoms, 29.0% chlorophytes, and 11.4% cyanobacteria in the community composition. There were 122 species belonging to 66 genera of 8 phyla in Shuanglong Lake, dominated by the same three groups with 19.7% diatoms, 48.4% chlorophytes, and 22.2% cyanobacteria. The densities of total algae and individual dominant groups were all much higher in the lake. More species of diatoms were found in the river-lake segment; whereas more chlorophyte species and cyanobacteriaum species were in the lake. There were 17 dominant species including 8 diatoms, 4 chlorophytes, 3 cyanobacteria and 2 cryptophytes in the river-lake segment, and 21 species in the lake, including 2 diatoms, 9 chlorophytes, 6 cyanobacteria, 3 cryptophytes and a dinoflagellate. In eutrophic conditions, chlorophytes and cyanobacteria mayproliferate in a lake-type area and diatoms may cause algal bloom in a relatively faster-flow lake-river type area.