The middle and lower Yangtze (MLY) floodplain has one of the most densely distributed lake clusters in China but suffered from long-term lake reclamation and wetland degradation due to intensive cultivation, fish rearing, and urban expansion over the past several decades. As a land-use alternation to support human life, the conversion of lakes to cropland, aquaculture ponds, and human settlements provides essential ecosystem goods at the expense of the deterioration of wetland environment. To quantify the driving factors of lake changes, we investigated the land-use transitions from lakes (≥1 km2) between 1975 and 2015 using Landsat remote sensing data. We found that the dramatic decline in lake area (a net decrease of 13.8 ± 1.4%) over the four decades was largely attributed to human-induced transformation from lakes to cropland, fish ponds, and built-up areas, accounting for 34.6%, 24.2%, and 2.5% of the total area reduction, respectively. The remaining loss, associated with vegetation (37.3%) and bare land (1.4%) and coming mainly from China's two largest freshwater lakes (Poyang and Dongting), can be explained by climate variation, sediment deposition, and hydrological regulation. These findings shed new light on the quantitative impacts of human activities and climate variation on lake changes and provide a scientific foundation for wetland management decision-making.