Between May 2006 and November 2009, we investigated the relationship between fluctuations in environmental factors and phytoplankton communities in Saemangeum Artificial Lake, South Korea. Nutrient concentrations in the lake increased because of the inflow of water from Mankyung and Dongjin Rivers during the summer rainy season; in particular, high concentrations were detected at an inner zone close to the estuaries. During the summer rainy season, salinity at the inner zone reduced more rapidly than that at the other zones, and it was similar to the changes in nutrient concentrations. Variations in phytoplankton communities were caused by fluctuations in environmental factors: the abundance of phytoplankton at the inner zone was higher than that at the other zones. Diatoms were the dominant species in the phytoplankton communities. A small centric diatom, Skeletonema costatum like species, was predominant, with a mean abundance of 19.5% in Saemangeum lake. Because of accelerated eutrophication in the lake, phytoplankton abundance increased continuously and the total number of species present in the community decreased. In particular, some dinoflagellates could intermittently cause red tides during low temperature and salinity conditions (at the inner zone). In 2006~2007, a red tide-forming dinoflagellate, Prorocentrum minimum, was the predominant species, while Heterocapsa triquetra, Karlodinium veneficum, and Heterocapsa rotundata were the newly recorded species in late 2008 to early 2009. Therefore, the dynamics of phytoplankton communities under the perennially eutrophic conditions in Saemangeum lake appear to be primarily affected by changes in water temperature and salinity. In particular, the growth of harmful algae may have been accelerated by the low salinity and temperature conditions during the spring season at the inner zone.