Backflow, the temporary reversal of discharge at the outlet of a lake, is an important mechanism controlling flow and transport in many connected river–lake systems. This study used statistical methods to examine long-term variations and primary causal factors of backflow from the Yangtze River to a laterally connected, large floodplain lake (Poyang Lake, China). Additionally, the effects of backflow on the lake hydrology were explored using a physically based hydrodynamic model and a particle-tracking model. Although backflow into Poyang Lake occurs frequently, with an average of 16 backflow events per year, and varies greatly in magnitude between years, statistical analysis indicates that both the frequency and magnitude of backflow reduced significantly during 2001–2010 relative to the previous period of 1960–2000. The ratio of Poyang Lake catchment inflows to Yangtze River discharge can be used as an indication of the daily occurrence of backflow, which is most likely to occur during periods when this ratio is lower than 5%. Statistical analysis also indicates that the Yangtze River discharge is the main controlling factor of backflow during July to October, rather than catchment inflows to the lake. Hydrodynamic modelling reveals that, in general, backflow disturbs the normal northward water flow direction in Poyang Lake and transports mass ~20 km southward into the lake. The effects of backflow on flow direction, water velocities and water levels propagate to virtually its upstream extremity. The current study represents a first attempt to explore backflow and causal factors for a highly dynamic floodplain lake system. An improved understanding of Poyang Lake backflow is critical for guiding future strategies to manage the lake, its water quality and ecosystem value, given proposals to modify the lake–river connectivity.