Backflow from the Yangtze River to Poyang Lake occurs frequently due to their different flood seasons. Based on the reasons for and time period of backflow, this study estimated the spatial-temporal extent and the change of water clarity influenced by sediments within the backflow and northern Poyang Lake using time-series Moderate Resolution Imaging Spectroradiometer (MODIS) images. The results revealed that the sediments from backflows together with dredging activities in the northern Poyang Lake not only affected the northern Poyang Lake, but also influenced the central and southern Poyang Lake and the Poyang Lake national nature reserve, and resulted in great decline of water clarity in the regions influenced, which could seriously affect the lake ecosystem. The results indicated that MODIS images have potential for monitoring the distribution of sediments from backflows and dredging activities. However, the potential is limited because of the frequent cloud cover in the study area and the characteristics of backflow itself. The dredging activity combined with backflows might have great negative impacts on the Poyang Lake ecosystem, and it would be worthwhile to explore the possible impacts in order to develop scientific knowledge to support the decisions, which need to be made by the responsible authorities for deciding how to rationally manage this unique lake ecosystem.