This study on epipelic algal flora and its seasonal variations in the Kucukcekmece Lagoon, Turkey was carried out between May 2001 and June 2002. A total of 109 species were identified, most of which belonged to Bacillariophyta (64 taxa). Other taxa identified included members of Cyanophyta (26), Chlorophyta (13), Euglenophyta (5) and Phaeophyta (1). Bacillariophyta were dominant in terms of species number and abundance at five stations. The seasonality of epipelic algal flora was different at all stations. Lower total cell numbers were registered at St. 5. Pennate diatoms especially Amphora spp.. Navicula spp., Nitzschia spp. and Synedra spp. were dominant during the sampling period. Cluster analysis was applied to the epipelic algal community and produced two major groups reflecting the importance of seasonal variation on the epipelic algal flora.