To assess the impacts of habitat filtering on taxonomical and functional compositions of fish communities, we conducted a fish survey in four typical microhabitats(i.e., littoral zone, open water, lake inlets and river channel) of the Lake Caizi, lower reaches of the Yangtze River Basin, in June-August, 2018. Forty-three fish species belonging to 5 orders and 31 genera were caught in total. More riverine species lived in the river channel microhabitat, while less of lacustrine biota, river-lake migratory and riverine species lived in the littoral zone microhabitat. Further analysis revealed that there exist significant differences in fish community compositions among the four microhabitats. Meanwhile, the dominant species of river channels were Sarcocheilichthys sinensis, Saurogobio gymnocheilus and Saurogobio dabryi, while Aristichthys nobilis, Ctenopharyngodon idellus, Hypophthalmichthys molitrix were dominant in the open water of the lake. In addition, Hemiculter leucisculus were found dominated in the littoral zone. By using one-way PERMANOVA analysis, we found both richness index and Shannon-Wiener index in littoral zone were significantly lower. In contrast, indices of functional diversity were stronger predictors for the impacts of habitat filtering on floodplain fishes, which showed that the RaoQ index in littoral zone was significantly lower while the FDiv index in river channel was significantly higher than those in the other three microhabitats.