We characterized phytoplankton community succession at different depths of a shallow hypertrophic reservoir in relation to physical and chemical environmental variables. The phytoplankton community was sampled biweekly at three different water depths (surface, middle and bottom) in the reservoir from November 2002 to February 2004. A range of 18 environmental variables including temperature, electrical conductivity (EC), total phosphorus (TP) and total nitrogen (TN) were measured to assess their influence on phytoplankton community succession. As well, combined multivariate analyses with a cluster analysis and a nonmetric multidimensional scale (NMDS) were conducted. Microcystis aeruginosa was the dominant species in all seasons except spring. Thus, Cyanophyceae was a dominant taxonomic group. In spring, Bacillariophyceae dominated, followed by Cryptophyceae and Chlorophyceae. The succession was relatively delayed at the middle and bottom layers compared with at the surface layer. Abundance and species richness of phytoplankton were also higher in the surface layer than in the bottom layer. Cluster analysis classified the phytoplankton community into four clusters at each depth, and the changes were also well reflected in the NMDS ordination. Each cluster showed seasonal patterns characterized by indicator species, as well as environmental variables such as temperature, conductivity, and nutrients including N and P. Seasonal dynamics of the phytoplankton community was the strongest at the surface layer and weakest at the bottom layer. These depth-variable environmental variables are likely to be the key factors driving changes in the phytoplankton community composition.