Flood pulse influence on phytoplankton communities of the Aksu Stream, Giresun, Turkey were studied between December 2008 and December 2009. The phytoplankton communities consisted of 54 species. The number of species and diversity of phytoplankton showed seasonal variation, being high in rainy season. As a consequence of the flood which occurred twice in July 2009, phytoplankton environment changed physically and chemically, which resulted in an alteration in the composition of phytoplankton community. The phytoplankton community that existed previous to the flood event, had been dominated by Hantzschia amphioxys but was replaced by Nitzschia palea and a teratological form of Fragilaria sp. Presence of teratological form of diatom in the stream indicated unfavourable conditions in this region.