Abstract: Jajerood river is one of the freshwater river in Iran. Seasonal changes in phytoplankton composition and physico-chemical factors affecting these parameters were investigated in this study. Qualitative phytoplankton and nutrient analysis were carried out between 2005 and 2006 at 19 sampling stations of Jajerood, situated in the north-eastern of Tehran. A total of 53 taxa were determined, belonging to four algae classes: Bacillariophyceae, Chlorophyceae, Cyanophyceae and Dinophyceae. Bacillariphyceae appeared to be the dominant group in terms of total genus number during the study period. The number of phytoplankton genus was high in summer and quite low in winter. The highest phytoplankton diversity determined in summer was due to the increase in the numerical of Cymbella from the diatoms. Phytoplankton diversity declined to the lowest level in the winter. The lowest and highest concentration of NO3 and PO4 were 1.9 and 8.5 μg L-1 and 0.05 and 0.76 μg L-1, respectively.