Understanding the effects of disturbance regimes on community assembly is an essential issue in community ecology. Yet, little is known about how water regimes drive community assembly considering functional facets in aquatic communities. We detected functional trait patterns of amphibious plant communities and checked the effects of inundations on these patterns, using null model analyses based on observational data of 20 Yangtze River floodplain lakes. Amphibious plant communities in the study lakes were dominated by perennials and a large proportion (61.2%) of communities were species-poor (species richness < 3). Null model analyses based on both incidence and biomass data showed 95.6% species-rich communities (species richness ≥ 3) presented randomness trait patterns. A higher proportion of randomness was found in the post-flood (98.8%) than pre-flood (89.7%) communities, and randomness tended to be more important as inundation increased. We showed for the first time the effects of periodic inundations on trait patterns of amphibious plants in floodplain lakes. Our results suggested that randomness would be common and important at a fine scale even in highly disturbed habitats. We further put forward a new conceptual framework regarding the underlying assembly mechanisms that water regimes drove aquatic plant communities in river floodplain ecosystems.