Water level fluctuations between wet and dry seasons, assisting by lateral connectivity, play a fundamental role in underpinning the composition and distribution of fish fauna in floodplain lakes. The ecotone floodplains between the floodplain rivers and lakes are generally considered as the key areas where witness the exchange of fish species and the variations of biodiversity. However, the study of changes in taxonomic and functional diversity of fish communities in the ecotone floodplain in response to water level fluctuations is limited. Here we address this issue by measuring temporal (dry and wet seasons) and spatial (lotic and lentic habitat patches) changes in taxonomic and functional diversity of fish communities in the ecotone floodplain between the Yangtze River and Lake Caizi. A total of 52 species belonging to 37 genera, 12 families and 6 orders were collected in our study. Among them, there were significant differences in species number between wet and dry seasons, with 50 species and 42 species collected respectively. On the other hand, there was no significant difference in the number of species between lentic and lotic habitat patches, with 47 species and 48 species collected respectively. In comparison with wet season, the species richness, weight, abundance and importance value percentage of riverine species decreased by 7.3%, 6.3%, 14.4% and 12.0% in dry season. In comparison with lentic habitat patches, the species richness, weight, abundance and importance value percentage of riverine species increased by 5.3%, 14.6%, 18.0% and 22.3%. The fish fauna differences between seasons (dry and wet) and habitat patches (lentic and lotic) were determined by the abundance of Pseudorasbora parva, Saurogobio dabryi, Hemiculter leucisculus, Cyprinus carpio, Carassius auratus, Coilia brachygnathus, Pseudobrama simony, Culter ilishaeformis, Culter dabryi, Saurogobio gymnocheilus and Acheilognathus gracilis. Important value analysis showed that the dominant species of fish in lentic habitat patches and dry season were similar, and the dominant species of fish in lotic habitat patches and wet season were similar as well. The dominant species in wet season and lotic habitat patches were P. parva, S. dabryi, S. gymnocheilus and C. brachygnathus, while the dominant species in dry season and lentic habitat patches were C. carpio, C. auratus, H. leucisculus and P. simoni. Two-way ANOVA analysis indicated that one taxonomic diversity indices (Richness) and three functional diversity indices (FRic, FDiv and FDis) significantly differed between wet and dry seasons. Taxonomic richness, functional richness, functional divergence and functional dispersion were significantly higher in wet season than in dry season. Meanwhile, the functional richness was significantly higher in lentic than in lotic habitat patches. Functional diversity exhibited higher sensitivity than the traditional taxonomic diversity, since three functional diversity indices showed significant variations between wet and dry seasons. Meanwhile, our study highlight important functional recruitments of fish assemblages triggered by seasonal flood pulses.