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Maintaining moderate levels of aquatic plant cover in agricultural reservoirs is an important issue because aquatic plant development is closely related to diverse ecosystem functions, including the regulation of the microconditions of the air-water environment, the production of food sources, and the structuring of physical habitats. We analyzed annual changes in aquatic plant cover in the Junam reservoirs using remote sensing images and field-survey data. We established a time series of aquatic plant cover using satellite images, aerial photography, and field-survey data from 1997 to 2016. We assessed the relationship between aquatic plant cover and reservoir environmental conditions. No monotonic trend in aquatic plant cover was observed during the 20-year study period. However, we found that the total aquatic plant cover was influenced by a complex combination of meteorological (winter temperature and wind speed), hydrological (water level), and physicochemical (conductivity, N:P ratio) factors for the reservoir. We further suggest a collective management scheme focused on nutrient and water-level conditions to control the overgrowth of aquatic plants in agricultural reservoirs.