Phytoplanktons are the first bio- indicators of pollution in aquatic ecosystems. Phytoplankton assemblage and aquatic ecosystems are always influenced by environmental factors therefore these environmental changes and threats must be understood in any ecosystem. Phytoplankton are inexpensive and readily available bio- indicators. In the present study, phytoplankton were used to study the Sefid Rud River (the south Caspian Sea), in Iran. Three sampling sites were selected up to 25- 30 km from the River estuary. Samplings were carried out from June through September 2009. Phytoplankton samples were collected by phytoplankton sampler net with mesh size of 25?m. Water parameters including transparency, temperature, water velocity and pH were measured during the survey. Mean water temperature was 26.9 ? 7.7 ?c, velocity 0.13 ? 0.01 m/s, Secchi disk transparency and pH were 45cm and 7.4, respectively. Phytoplankton assemblage comprised Bacillariophyceae (61.2?), Chlorophyceae (31.6?), Euglenophyceae )5.0?) and Cyanophyceae (2.23?). Significant differences were observed in diversity and abundance of four main groups of phytoplankton between sampling stages. Significant positive correlations were detected between transparency and abundance of Chlorophyta, while negative correlations were found between transparency and Euglenophyceae abundances. The highest abundance of Euglena and Phacus (Euglenophyceae) occurred at high turbidity while maximum abundance of Pediastrum and Scenedesmus (Chlorophyceae) correlated with high water transparencies. Genus Oscillatoria (Cyanophyceae) was observed (abundance 18?) only in station 2 and influenced by agricultural activities. The study showed that phytoplankton are suitable bio- indicators of environmental changes which may threaten the Sefid Rud River and the Caspian Sea.