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Abstract In spring 2011, an unprecedented flood hit the complex eastern United States (U.S.)–Canada transboundary Lake Champlain–Richelieu River (LCRR) Basin, destructing properties and inducing negative impacts on agriculture and fish habitats. The damages, covered by the Governments of Canada and the U.S., were estimated to C$90M. This natural disaster motivated the study of mitigation measures to prevent such disasters from reoccurring. When evaluating flood risks, long‐term evolving climate change should be taken into account to adopt mitigation measures that will remain relevant in the future. To assess the impacts of climate change on flood risks of the LCRR basin, three bias‐corrected multi‐resolution ensembles of climate projections for two greenhouse gas concentration scenarios were used to force a state‐of‐the‐art, high‐resolution, distributed hydrological model. The analysis of the hydrological simulations indicates that the 20‐year return period flood (corresponding to a medium flood) should decrease between 8% and 35% for the end of the 21st Century (2070–2099) time horizon and for the high‐emission scenario representative concentration pathway (RCP) 8.5. The reduction in flood risks is explained by a decrease in snow accumulation and an increase in evapotranspiration expected with the future warming of the region. Nevertheless, due to the large climate inter‐annual variability, short‐term flood probabilities should remain similar to those experienced in the recent past.