The relationships between water discharge, temperature, total dissolved solids (TDS) conductivity, turbidity, nitrate, ammonium, phosphate and the seasonal dynamics of phytoplankton assemblages of two inlets of a shallow hypertrophic lake (Lake Manyas, Turkey) were studied between January 2003 and December 2004. The results showed that different levels of water discharge, turbidity, conductivity, TDS and nutrients could lead to the development of significantly different phytoplankton assemblages in inlets of shallow hypertrophic lakes. The multiple regression analysis identified water discharge, turbidity and water temperature as the driving factors behind the dynamics of phytoplankton biovolume in the studied inlets. The first two axes of Canonical Correspondence Analysis (CCA) explained 78% of the total variance in dominant phytoplankton species at Siğirci Inlet and 88% at Kocaçay Inlet, respectively. The purpose of this study was to determine the relationships between water discharge, temperature, conductivity, turbidity, pH, TDS, nitrate, ammonium, phosphate and the seasonal dynamics of phytoplankton assemblages of two inlets of the shallow hypertrophic Lake Manyas, Turkey by means of multivariate statistical analysis.