This study aimed to determine the seasonal variations in the growth and species composition of phytoplankton in Lake Paldang, South Korea’s largest freshwater body, based on environmental factors. Weekly surface water samples were collected and analyzed for three years (2015–2017). A total of 160 species of phytoplankton were distributed across eight divisions. Diatoms were dominant in all seasons except summer and their seasonal equivalents. All seven indices—Shannon, equitability, Simpson, Menhinick, evenness, dominance, and Berger-Parker—presented a clear trend in September, which may be attributed to rainfall in July. Canonical correspondence analysis (CCA) was employed to analyze the relationship between the occurrence and the abundance of phytoplankton species and environmental factors. The results showed that WTE, TP, PO4-P, and rainfall were negatively correlated with Ulnaria acus, Asterionella formosa, and Stephanodiscus hantzschii, whereas Scenedesmus sp. and Merismopedia tenuissima presented positive correlations. Microcystis demonstrated positive correlations with TOC, NH3-N, and HRT, and appeared primarily in the summer and fall of 2015, a dry season. According to the Palmer pollution index, which is calculated based on phytoplankton species, Lake Paldang showed no signs of pollution for the top 99.8% of phytoplankton species, but was evaluated as organically polluted for overall phytoplankton, especially in spring and summer.