This study investigated seasonal variations in phytoplankton community composition and physicochemical water quality across 90 lakes in South Korea surveyed 2022 to 2024, and examined their relationships with environmental factors. Over the course of four seasons, a total of 952 phytoplankton taxa were identified, with Bacillariophyta (diatoms) and Chlorophyta (green algae) accounting for 64.2% of the total species richness. Diatom species such as Aulacoseira granulata, Fragilaria crotonensis, and Cyclotella meneghiniana were frequently observed regardless of season. In terms of cell density, Cyanophyta were dominant, comprising 85.1% on average, with particularly high summer densities driven by blooms of Microcystis aeruginosa and Aphanizomenon sp. In contrast, diatoms accounted for the highest relative abundance in winter (54.1%). Canonical correspondence analysis (CCA) revealed that Cyanophyta and Chlorophyta were positively correlated with water temperature, TP, COD, and Chl-a, whereas Bacillariophyta and Cryptophyta showed negative correlations with these variables. These results indicate that phytoplankton communities in Korean lakes are highly responsive to variations in temperature and nutrient concentrations, and that summer rainfall-driven nutrient inflow plays a critical role in triggering cyanobacterial blooms. This study provides a scientific basis for understanding seasonal ecosystem dynamics in Korean lakes and offers foundational data for eutrophication management and the development of biological water quality assessment indices.