•FAV and SAV covers in Taihu Lake decreased rapidly after 2012.•Controlling factors of FAV and SAV were clarified.•Harvesting activity was mainly driving factor of the loss of FAV.•Water eutrophication should be responsible for the loss of SAV. A rapid degradation of aquatic vegetations in Taihu Lake has roused a wide attention in recent years. Giving large-scale harvesting activity on aquatic vegetation since 2012, whether water eutrophication or the human harvest activity induced the degradation remains controversial and unclear. In this study, based on Landsat and HJ-CCD data acquired from 1984 to 2016 and a 12-year field observation (2005–2016) of water quality, a method was proposed to quantitatively assess impacts of harvesting activity and water quality change on degradations of both floating-leaved aquatic vegetation (FAV) and submerged aquatic vegetation (SAV) in Taihu Lake. First, areas of FAV and SAV covers from 1984 to 2016 in Taihu Lake were mapped using the satellite data, and then the mapped areas were modified to those on a reference date by using phenological curves of FAV and SAV covers. Next, correlations between water quality data and FAV and SAV covers were analyzed by using Pearson correlation analysis based on the data before implementing the human harvesting activity (i.e., before 2012), and multiple general linear models were established based on the selected water quality variables with p-value <0.01 for estimating covers of FAV and SAV from 2012 to 2016. Finally, based on the predicted areas of FAV and SAV covers by the models and the modified areas mapped from satellite data, the influences of water eutrophication and the human harvesting activity on the degradation of FAV and SAV covers were quantitatively assessed. The results indicated that (1) FAV cover exhibited a significant increase from 1984 to 2011 and then a rapid decrease, while SAV cover increased significantly before 2003 and then obviously declined; (2) water level (WL) and total nitrogen (TN) showed significantly negative correlations with FAV and SAV covers, while secchi disk depth (SDD) and SDD/WL had significantly positive correlations with FAV and SAV covers; (3) the human harvesting activity made a major contribution to the loss of FAV cover, and the degradation of SAV cover was mainly due to an increased lake eutrophication and deteriorated underwater light environment. The findings derived from this study could offer a guidance for Taihu Lake ecological restoration and effective management.