The rivers and lakes of Japan have had a wide range of shoreline modifications for flood control and stabilization, but the effects of this on the ecology of Japanese eels, Anguilla japonica, is not known. To clarify possible effects of riverbank modifications on yellow-phase Japanese eels in the lower Tone River, Japan, the abundance, condition factor and stomach contents were investigated using 586 eels collected in both revetment and natural shore areas at four sites. Eel abundances and their condition factors were higher in the natural shore areas than those of revetment areas at the three freshwater sites, and the smallest sizes of eels appeared to prefer the natural areas at all sites. The number of feeding eels, their food consumption, and the diversity of consumed prey were also generally greater in the natural shore areas than in the revetment areas. Other differences in diet were observed, such as terrestrial oligochaetes only being eaten by eels at the freshwater river natural shore areas and bivalves being eaten more in the revetment areas of those sites. In contrast, in the brackish habitat eels appeared to be less affected by concrete revetment with wave-dissipating tetrapod blocks. The range of differences found between the freshwater sampling areas suggest that revetment shorelines are used less by eels, particularly smaller eels, when natural shore areas are available, and eels that live near revetment have a lower abundance and diversity of prey to feed on.