We investigated seasonal algae variability and its influence on water quality in an agricultural reservoir. We observed that maximal total phosphorus (TP) loads were 1,715 kg from farmland in September, which changed the ecosystem in the reservoir. At this time, Dictyosphaerium pulchellum as green algae dominated. Aulacoseira ambigua as diatom became the most dominant from November 2010 to May 2011. The diatom was sensitive to water temperature. Microcystis spp. and Oscillatoria spp. as cyanobacteria were dominant during summer and fall, and sank down to the sediment during winter and spring. Increasing water temperature during summer causes anaerobic conditions in the sediment, leading to regrowth of cyanobacteria. With regard to the ratio of total nitrogen (TN) to TP, green algae and cyanobacteria were dominant at TN:TP ratios less than 20-30. Diatoms were dominant at TN:TP ratios greater than 30-40. Statistical analysis indicated that diatom growth was dependent on water temperature and TN concentration. TP concentration and water temperature were the key factors for the growth of cyanobacteria and green algae. From these results of this study, the management of land-use was an important parameter for improving water quality in the agricultural reservoir.