In floodplains, which are highly modified and less inundated, trees are expanding, thus raising concerns regarding their impact on freshwater organisms. We analyzed the relationship between forest expansion and the change in Odonata (dragonflies and damselflies) assemblage over an extended period of time in the floodplain with ponds of the Kiso River, central Japan. In the 1970s, the ponds were mainly surrounded by grasslands, and approximately 80% of Odonata species were non-forest species. However, the number of forest species increased and that of non-forest species largely decreased with the forest expansion over the past five decades, resulting in almost a similar number of forest and non-forest species in 2021. Whereas the abundance of the non-forest species had been greater than that of the forest species until the 2000s, the difference has been much smaller in the 2010s, and the non-forest species occupied approximately only 30% of the number of individuals in 2021. The forest expansion may have reduced the open-lentic habitats for the non-forest species, which require riparian grasslands for resting, foraging, and reproduction, and may disturb the immigration of non-forest species from the adjacent rice paddy fields and rivers. The development of canopy cover over the waterbodies may have decreased the light and temperature above and within the ponds, which might have caused a decline in species that prefer warm and open-water environments. Maintaining shifting-mosaic patterns of vegetation around the floodplain waterbodies through active management may be effective in conserving floodplain Odonata communities, including both forest and non-forest species.