Since the early 1950s, the development of human settlements and over-exploitation of agriculture in the China side of the Amur River Basin (CARB) have had a major impact on the water environment of the surrounding lakes, resulting in a decrease of aquatic vegetation. According to the United Nations Sustainable Development Goals, a comprehensive understanding of the extent and variability of aquatic vegetation is crucial for preserving the structure and functionality of stable aquatic ecosystems. Currently, there is a deficiency in the CARB long-sequence dataset of aquatic vegetation distribution in China. This shortage hampers effective support for actual management. Therefore, the development of a fast, robust, and automatic method for accurate extraction of aquatic vegetation becomes crucial for large-scale applications. Our objective is to gather information on the spatial and temporal distribution as well as changes in aquatic vegetation within the CARB. Utilizing a hybrid approach that combines the maximum spectral index composite and Otsu algorithm, along with the integration of convolutional neural networks (CNN) and random forest, we applied this methodology to obtain an annual dataset of aquatic vegetation spanning from 1985 to 2020 using Landsat series imagery. The accuracy of this method was validated through both field investigations and Google Images. Upon assessing the confusion matrix spanning from 1985 to 2020, the producer accuracy for aquatic vegetation classification consistently exceeded 87%. Further quantitative analysis unveiled a discernible decreasing trend in both the water and vegetation areas of lakes larger than 20 km² within the CARB over the past 36 years. Specifically, the total water area decreased from 3575 km² to 3412 km², while the vegetation area decreased from 745 km² to 687 km². These changes may be attributed to a combination of climate change and human activities. These quantitative data hold significant practical implications for establishing a scientific restoration path for lake aquatic vegetation. They are particularly valuable for constructing the historical background and reference indices of aquatic vegetation.