Phytoplankton and epipelon assemblages form the main constituents, and they are producers in aquatic ecosystems, such as streams and rivers. This study was carried out between May 2008 and April 2009 to determine the impacts of polluted water on species variations, compositions, and community metrics in phytoplankton and epipelon at six stations on Ankara Stream. A total of 231 taxa were recorded during the study period, with 131 Bacillariophyta, 3 Charophyta, 41 Chlorophyta, 30 Cyanobacteria, 25 Euglenophyta, and 1 Ochrophyta. Heterogeneity of the stream stations was determined by the use of hierarchical cluster analysis (HCA). Community metrics were compared by using non-parametric tests, while canonical correspondence analysis (CCA) was used for the relationships between environmental variables and species. Variations in water quality and species composition along the stream flow revealed a significant spatial heterogeneity (p<0.05). However, the upper stations of the stream were represented by unpolluted water quality with low nutrients and conductivity, and the mid- and downstream stations were characterized by high concentrations of ammonia (up to 60mgL(-1)) and o-phosphate (up to 25mg/L), with low concentrations of dissolved oxygen (<1mgL(-1)). The results, clearly supported by indicator taxa, showed that various domestic and industrial discharges affected the increase in pollution and the spatial heterogeneity. The findings obtained in this study will contribute to future improvements in Ankara Stream watershed studies.