The seasonal effects of nutrient loading from migratory waterfowl on water and the successive changes of the aquatic ecosystem based on each biomass of phytoplankton, zooplankton and submerged macrophytes were surveyed in Tsubasa Pond, Yonago Waterbird Sanctuary, Japan. The pond's water quality gradually deteriorated with the influx of migratory waterfowl. The concentration of total nitrogen corresponded rapidly with waterfowl biomass. Peak concentrations of total phosphorus and chlorophyll a (Chl.a) were observed about one month later when the migratory waterfowl had flown away. After one month, the peak concentration of Chemical Oxygen Demand (CODMn) appeared. Thus, the water quality of the pond had gotten worst after the waterfowl had flown away. Then, decrease of Chl.a concentration and increase of zooplankton density were observed in spring. In summer, the population of a submerged macrophyte increased temporarily and water quality recovered. These results indicated that the primary producer in the bird sanctuary pond alternated from phytoplankton to submerged macrophyte in one year.