Aquatic vegetation in shallow freshwater lakes are severely degraded worldwide, even though they are essential for inland ecosystem services. Detailed information about the long term variability of aquatic plants can help investigate the potential driving mechanisms and help mitigate the degradation. In this paper, based on Google Earth Engine cloud-computing platform, we made use of a 33-year (1987–2019) retrospective archive of moderate resolution Landsat TM, ETM + and OLI satellite images to estimate the extent changes in aquatic vegetation in Longgan Lake from Middle Yangtze River Basin in China using the modified enhanced vegetation index, including emerged, floating-leaved and floating macrophytes. The analysis of the long term dynamics of aquatic vegetation showed that aquatic vegetation were mainly distributed in the western part of the lake, where lake bottom elevation ranged from 11 to 12 m, with average water depth of less than 1 m in spring. The vegetation area variation for the 33-year period were divided into six stages. In years with heavy precipitation, the vegetation area decreased sharply. In the following years, the area normally restored. Aquatic vegetation area had a significant negative correlation with the spring water level and summer water level. The results showed that aquatic vegetation was negatively affected when water depth exceeded 2.5 m in May and 5 m in summer. It is recommended that water depth remain close to 1 m in spring and close to 3 m in summer for aquatic vegetation growth. Our study provide quantitative evidence that water-level fluctuations drive vegetation changes in Longgan Lake, and present a basis for sustainable lake restoration and management.