Wetlands are at high risk of degradation worldwide, but the driving mechanisms at different spatiotemporal scales vary and remain unclear. In this study, we used Landsat images from 1986 to 2016 to assess variations in natural wetlands in the five sub-watersheds of the Dongting Lake Watershed (DTLW): the Xiang River Watershed (XRW), Zi River Watershed (ZRW), Yuan River Watershed (YRW), Li River Watershed (LRW), and Dongting Lake Area (DTLA). We also explored the relationships between variations in wetland area and meteorological factors, along with anthropogenic factors. The total area of natural wetlands in the DTLW decreased by 124.12 km² (2.45%) over the study period, mainly due to the declines in lake and marsh areas. The wetland area decreased in the ZRW and DTLA, but increased in the other three. Mean annual precipitation (MAP) was highly variable over time, while mean annual temperature (MAT) increased significantly in all sub-watersheds. Overall, gross domestic product (GDP), population (POP), cultivated area (CA), and irrigation area (IA) increased from 1986 to 2016. MAT had the maximum correlation with lake and river area changes in the DTLW, while marsh area changes were best correlated with POP. The IA was the greatest contributor of lake area change in XRW, LRW, and DTLA, while the dominant factor for river area change differed by sub-watershed. Overall, the most influential factors were meteorological changes in the DTLW as a whole, while anthropogenic activities were more important at the sub-watershed scale.