In this study, extensive investigation was done on the changes in bottom topography across the Lake Poyang through geographical information systems(GIS) techniques and comparison of underwater topography data of 1980, 1998 and 2010. Possible mechanisms behind the topographic changes were also discussed based on watershed hydrological data(e.g. sediment transport, soil erosion and reservoir construction). The results showed that (1) the main water body region was obviously deposited with an average deposition value of 0.82 m during 1980-1998. These alterations of bottom topography were frequently caused by the increased soil erosion in the upstream of the basin. (2) During 1998-2010, the deposition trend of the bottom topography among Lake Poyang was slowed down to some extent. This was probably caused by the afforestation and reservoir construction program. However, in this period, bottom topography in the channel entrance was decreased remarkably with the average declining rate of 30.75 cm/a. The increases in flow discharge and gravel extraction have been considered as the main causes of this topographic change in the region. (3) In recent 30 years, the changing trends of deposition/erosion among five rivers' alluvial cone were different. Bottom topography elevation in Xiushui, Fuhe and Ganjiang alluvial cone expressed gradually decreasing trend, while Raohe alluvial bay showed a rising tendency as a whole. The results of the study are of great theoretical and practical significance to water resources reasonable utilization, dam construction and shipping management across the Lake Poyang.