Abstract Driven by seasonal flood pulses, fish species inhabiting floodplains migrate between lotic and lentic habitat patches to complete their life histories, which can result in the severely species turnover or nestedness. However, these spatiotemporal dynamics of fish metacommunities (beta diversity) were barely quantified. Previous studies either based on species incidence data in calculating beta diversity or solely focus on partial habitat (lotic or lentic) were widely criticized for their misleading results. Here, we addressed the issue by comparing the taxonomic and functional differences in beta diversity and the turnover and nestedness components between wet and dry seasons in the Yangtze-Caizi transitional floodplain. The calculating of beta diversity based on both incidence and abundance data were also compared respectively to test their sensitivity in revealing fish metacommunity dynamics triggered by flood pulses. Regionally in the studied transitional floodplain, we detected significantly taxonomic and functional homogenization of fish assemblages triggered by floods in the high-water period. Then locally within the lotic habitats, our results demonstrated significantly higher overall beta diversity and the turnover components in both the high and low waters. Meanwhile, the significantly higher Local Contributions to Beta Diversity (LCBD) also indicated the higher uniqueness of lotic habitats. These findings highlighted remarkably heterogeneous fish assemblages in lotic habitats, thus deserving higher conservation priority in contrast with lentic habitats. Comparing with classic incidence-based measurements, our results exhibited higher sensitivity of abundance-based approaches in revealing homogeneous or heterogeneous patterns of fish metacommunities influenced by floods. Our results highlighted the importance of employing abundance-based data to measure beta diversity within small spatial extents.