In environmental transition zones, the environment fluctuates between two different types of environments in time, and the seasonal change is more pronounced.In this study, we examined seasonal shift in the spatial structures of biotic assembly in the floodplain waterbodies, lotic-lentic transition zone, and examined biological processes behind the seasonal reassembly.　As results, we observed clear seasonal reassembly of biological communities in lotic-lentic transition zones in a floodplain. While the biological communities were largely driven by the landscape environmental gradient after the transition, the effect of the environmental gradient from lotic to lentic transition weakened over time, and the communities were reassembled based more on the local environments. Aquatic communities in the floodplain waterbodies were strongly influenced by the flood regime over the flood period, and exhibited spatial gradient along with hydrological connectivity gradient to the river over flood period. However, as many amphibian and aquatic insect larvae that consisted  the major members of the assembly metamorphose and emerge out of the water over the summer period, aquatic biota reassembled in different ways more strongly influenced by local environmental factors such as size of waterbodies, temperature  and dissolved oxygen level.