The Tohma Stream is among the most important tributaries of the transboundary Euphrates River. The aim of this work is to evaluate which are the most important environmental variables that might affect epilithic communities in Tohma Streams and species composition in microhabitats. A total of 89 taxa belonging to 4 phyla were identified in the study area (Bacillariophyta, Chlorophyta, Cyanobacteria and Charophyta). According to temporal and spatial heterogeneity of Tohma Stream, ecological indices of epilithic algal composition demonstrated significant differences at the 95% confidence level. Mean DIN: SRP< 10 ratio was recorded at sts 4, 5, 8 and 9 in dry and wet seasons. Mean DIN: SRP was detected 80.028 ratio due to excessive pollution runoff. There was a correlation between community diversity and Bacillariophyta which is the most abundance group. According to changes in the species level of community composition, stations have been separated into 2 main groups in UPGMA cluster analysis. Stl l was placed 2nd main group and this situation has also been confirmed in the RDA analysis due to Tohma Stream derived mainly from agricultural, domestic and organic runoffs from industrial zone were mostly higher than the other stations.