Summary Anthropogenically induced reduction in flood inundation frequency often leads to terrestrialisation, which accompanies establishment and expansions of tree cover on areas formerly with little or no trees. We tested hypotheses that terrestrialisation degrades habitat for freshwater mussels (Unionoida: Unio douglasiae nipponensis and Lanceolaria grayana) by changing the organic matter (OM) dynamics in floodplain backwaters. Stable isotope composition of seston, periphyton, fine and coarse benthic particulate OM (FBPOM and CBPOM) and mussel tissues was measured to understand OM dynamics and food webs in 14 backwaters in the middle segment of the Kiso River, Japan. Isotope ratios, C : N ratio and chlorophyll a as a proxy of food resource characteristics and the frequency of hypoxia were related to mussel growth rates. δ13C of seston, periphyton and FBPOM was low at sites with lower inundation frequency (a greater degree of terrestrialisation), whereas such a trend was not observed for CBPOM (i.e. riparian leaf litter). Mussels fed exclusively on seston or mixtures of seston and periphyton with their δ13C tracking fluctuations in food resources. Sestonic δ13C differences were attributed to changes in dominant carbon origin from predominantly river‐borne to autochthonous sources, while periphytic δ13C differences were possibly caused by a varying level of dependence on respiratory CO2. FBPOM‐δ13C differences were associated with a greater contribution of CBPOM to the FBPOM pool in infrequently flooded backwaters. Variability in mussel growth was more closely related to hypoxia than food resource characteristics. We inferred that terrestrialisation changes quality of seston and benthic detritus and degrades habitat conditions largely by accumulating riparian leaf litter in the benthic detrital pool and increasing the frequency of hypoxia. The removal of riparian trees may temporarily improve habitat condition in backwaters heavily affected by terrestrialisation. However, ecological integrity in the long run requires the recovery of the process that suppresses terrestrialisation, which includes restoration of incised channels and flood pulses.