Microplastic contamination is a challenge in aquatic systems. Among these, floodplains exhibit their cyclical hydrological patterns with substantial fluctuations in water levels caused by annual floods or discharges from rivers into lakes. The influence of water level fluctuation on microplastics within complex floodplain systems has received limited attention in existing studies. This study employs hydrological data and a physics-based hydrodynamic model to assess the effects of water level fluctuations on the transport and redistribution of microplastics within Poyang Lake from 2018 to 2025. High spatiotemporal distribution variability in microplastic concentrations was found within the flood and drought periods. Furthermore, the residence rate of microplastics was assessed based on the microplastic concentration variations in the computational time. A gradual drop in the average discharge rate of microplastics was assessed at the outlet of Poyang Lake. The microplastics are more likely to drain into the Yangtze River in the high water-level period. Meanwhile, under the influence of hydrodynamics, local topography, and water level fluctuation, an accumulation of microplastics appears on the shallow shoals of the western and eastern regions of Poyang Lake, especially in the Gan River. Overall, by means of numerical simulation, the aim of our study is to serve as a reference and advance our understanding of the transportation patterns of microplastics at the aquatic–terrestrial interface.