Water eutrophication is a significant environmental issue that impacts aquatic ecosystems worldwide. In this study, we aimed to investigate the relationships among the water physicochemical characteristics, phytoplankton community, and cyanotoxins in the Ubol Ratana Dam, Khon Kaen, Thailand, during the years 2022–2023 and to evaluate the relationships between changes in water parameters and the dynamics of the phytoplankton community under seasonal variations in the Ubol Ratana Dam. A total of 84 phytoplankton species belonging to 8 phyla were found in six different locations in the reservoir. Cyanobacteria (Cyanophyta) had the highest cell density (84.06%), with Microcystis aeruginosa being the dominant species. In terms of seasonality, the diversity indices, including Shannon‒Wiener and evenness values, were highest during summer and lowest during the rainy season, while species richness remained constant. Interestingly, the phytoplankton density was greater at the center of the dam and water outlet stations than that at the other stations, and these two areas also had the lowest nitrate and ammonium concentrations. Canonical correspondence analysis (CCA) explained 66.8%, 70.6%, and 63.8% of the total variation in the rainy, winter, and summer seasons, respectively. This indicates that nitrate and ammonium were factors that influenced phytoplankton growth. Correlation analysis revealed that the abundance of dominant cyanobacteria was positively correlated with temperature and orthophosphate content and negatively correlated with nitrate and ammonium content. Overall, nitrogen concentration mainly governed cyanobacterial blooms. These results suggest that relationships between physicochemical factors and the phytoplankton community significantly influence the seasonal variations in phytoplankton, providing valuable insights for future monitoring of phytoplankton blooms.