Anthropogenic disturbances pose significant threats to biodiversity. However, limited information has been acquired regarding the degree of impact human disturbance has on the β-diversity of plant assemblages, especially in threatened ecosystems (e.g., floodplains). In the present study, the effects of anthropogenic disturbance on plant communities of floodplain areas (the Miya River, Mie Prefecture, Japan) were analyzed. The taxonomic and functional β-diversity among different degradation levels were compared, and the differences were assessed by tests for homogeneity in multivariate dispersions. In addition, the effects of non-native species and environmental factors on β-diversity were analyzed. As revealed from the results, anthropogenic disturbance led to taxonomic homogenization at a regional scale. The increase in non-native invasions tended to improve homogenization, whereas at a low degradation level, the occurrence of non-natives species was usually related to taxonomic differentiation. Furthermore, though the increase in non-natives and environmental parameters significantly affected the β-diversity of the floodplain area, environmental factors may be of more crucial importance than biotic interactions in shaping species assemblages in this study. The previously mentioned result is likely to be dependent on the research scale and the extent to which floodplains are disturbed. Given the significant importance of floodplains, the significance of looking at floodplains in the different levels of degradation was highlighted, and both invasion of non-native species and environmental factors should be considered to gain insights into the response of ecosystems to anthropogenic disturbance. The findings of this study suggested that conservation programs in floodplain areas should place more emphasis on the preservation of natural processes and forest resources.