Study Region: Jupiá Hydropower Station, the junction of São Paulo and Mato Grosso, Brazil. Study Focus: During the flood season, a large amount of aquatic vegetation is brought to the front of the dam, which not only threatens the safety of the project but also causes internal pollution in the reservoir. This study combined the field data with the remote sensing technology to analyze the temporal and spatial succession of aquatic vegetation in the Jupiá Reservoir. The biomass inversion models were established to estimate the biomass of aquatic vegetation in the whole reservoir area. New hydrological insights: (1) The area of aquatic vegetation in rainy season could reach twice that in dry season. From 2018–2022, the total area of aquatic vegetation in the reservoir area showed an overall trend of increase. (2) The total biomass of floating vegetation and submerged vegetation in the reservoir area fluctuated little from 2018 to 2022, with an annual average of 32.14 × 104 t, of which the average biomass of floating vegetation only accounts for 23.5% of the total biomass. Submerged vegetation was an important object of aquatic vegetation management in this reservoir.