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The Shahid Rajaei Reservoir constructed for various purposes such as drinking water supply. In this context, and also because of the importance of the bloom events and eutrophication process in dams, this paper is to survey the relations between some of physicochemical parameters and phytoplankton composition and density, chlorophyll-a and some water quality indices (Trophic, Saproby, Shannon) using mono and multivariate statistical analysis. Water samples collected from 4 stations during May, June, July, August, September, November and February in 2012-2013. According to the results, the maximum concentration of dissolved inorganic nitrogen, chlorophyll-a, phytoplankton abundance, trophic and saproby indices observed in a month of summer which it was accompanied to the minimum value of species diversity index (Shannon). Pearson analysis revealed direct correlation between abundance of Goniaulax polyedra, Goniaulax digitale and trophic index. In the other words, higher abundance of the two species decreased the water quality. Also based on the PCA analysis, the significant correlation observed between abundance of Cyclotella meneghiniana with Shannon and saproby indices which were negative and positive, respectively. This result indicates to the relation of degradation of water quality with increasing the abundance of Cyclotella meneghiniana. Meanwhile, the presence of the three parameters (abundance of Cyclotella meneghiniana, Shannon and saproby indices) in first component of PCA indicated the important role of Cyclotella meneghiniana and two biological indices in determining of water quality in Shahid Rajaei Reservoir.