Progressive floodplain terrestrialization leads to the deterioration of floodplain ecosystems. Although the importance of hydrological connectivity between floodplain habitats and river channels for floodplain‐dependent organisms has been emphasized, less attention has been paid to the temporal relationship between habitat degradation and aquatic organisms. In this study, we examined temporal changes in mussel population structures and the hydrological connectivity of pond‐like floodplain water bodies (FWBs) in the terrestrialized floodplains of a lowland river in Japan. We tested the hypothesis that FWB habitats for mussels degrade over time, while newly formed FWBs contribute to providing recruitment sites for mussels. The habitat age for 53 FWBs was determined as of 2018, using historical aerial photographs. Inundation frequency, mussel abundance, and size structures (shell length) were also investigated in the FWBs in 2007 and 2018. Mussel abundance decreased with FWB aging (6–36 years), which coincided with a decrease in inundation frequency. In most existing FWBs, mussel abundance in all size classes decreased over the decade (2007–2018). In contrast, small individuals occurred in the newly formed FWBs at age 6, and in the existing FWBs where inundation frequency slightly increased over the decade (2007–2018), such FWBs were rare. In conclusion, the “young” and “rejuvenated” FWBs were found to be critically important for the recruitment and persistence of mussel populations. This suggests that the floodplain management strategy of “cyclic floodplain rejuvenation” could be applicable for mussel conservation in terrestrialized floodplains of lowland rivers.