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Abstract The Amazon floodplains represent important surfaces of highly valuable ecosystems, yet they remain neglected from protected areas. Although the efficiency of the protected area network of the Amazon basin may be jeopardized by climate change, floodplains are exposed to important consequences of climate change but are omitted from species distribution models and protection gap analyses.The present and future (2070) distribution of the giant bony‐tongue fishArapaimaspp. (Arapaimidae) was modelled accounting for climate and habitat requirements, and with a consideration of dam presence (already existing and planned constructions) and hydroperiod (high‐ and low‐water stages). The amount of suitable environment that falls inside and outside the current network of protected areas was quantified to identify spatial conservation gaps.We predict that climate change will cause a decline in environmental suitability by 16.6% during the high‐water stage, and by 19.4% during the low‐water stage. About 70% of the suitable environments ofArapaimaspp. remain currently unprotected. The gap is higher by 0.7% during the low‐water stage. The lack of protection is likely to increase by 5% with future climate change effects. Both existing and projected dam constructions may hamper population flows between the central, Bolivian and Peruvian parts of the basin.We highlight protection gaps mostly in the south‐western part of the basin and recommend the extension of the current network of protected areas in the floodplains of the upper Ucayali, Juruà and Purus rivers and their tributaries. This study has shown the importance of integrating hydroperiod and dispersal barriers in forecasting the distribution of freshwater fish species, and stresses the urgent need to integrate floodplains within the protected area networks.