The aim of this study was to determine the seasonal variation of phytoplankton in a connected river system, the Kirmir and its tributaries the Suveri and the Ilhan. The samples were collected from a total of ten selected stations on the main river and tributaries in November 2006, February, May and August 2007. A total of 57 phytoplankton species from Bacillariophyta, Chlorophyta, Chrysophyta, Cryptophyta, Cyanobacteria, Euglenophyta and Pyrrophyta were identified. Bacillariophyta species were dominant in all stations during the research period. Caloneis bacillum, Cocconeis placentula, Cyclotella meneghiniana, Diatoma vulgare, Gomphonema ventricosum, Nitzschia sigmoidea and Ulnaria ulna appeared at high densities in the samples. The maximum phytoplankton abundance was found in the Kirmir on all sampling dates. Furthermore, some species which are indicators of pollution were found in the Kirmir.