© 2018 Society for Conservation Biology Large dams provide vital protection and services to humans. However, an increasing number of large dams worldwide are old and not operating properly. The removal of large dams has excellent potential to restore habitat connectivity and flow regimes; therefore, projecting the related ecological consequences is an emerging need for water resource and ecosystem management. However, no modeling methods are currently available for such projections at the basin scale. We devised a scheme that integrates changes in flow regimes and habitat network structure into a basin-scale impact assessment of removal of large dams and applied it to the Nagara-Ibi Basin, Japan. We used a graph-theoretical approach and a hydrological model, to quantify changes in habitat availability for 11 freshwater fishes at the basin scale under multiple removal scenarios. We compared these results with the change predicted using a conventional scheme that considered only changes to the habitat network due to dam removal. Our proposed scheme revealed that an increase in flow variability associated with dam removal projected both positive and negative effects on basin-scale habitat availability, depending on the focal species, endangered species had a negative response to dam removal. In contrast, the conventional approach projected only positive effects for all species. This difference in the outcomes indicates that large-dam removal can have negative and positive effects on watershed restoration due to changes in flow regimes. Our results also suggest the effect of removal of large dams may depend on the dams and their locations. Our study is the first step in projecting ecological trade-offs associated with the removal of large dams on riverscapes at the basin scale and provides a foundation for future process-based watershed restoration.