AbstractAimNatural disaster risk reduction (DRR) is becoming a more important function of protected area (PAs) for current and future global warming. However, biodiversity conservation and DRR have been handled separately and their interrelationship has not been explicitly addressed. This is mainly because, due of prevailing strategies and criteria for PA placement, a large proportion of PAs are currently located far from human‐occupied areas, and habitats in human‐occupied areas have been largely ignored as potential sites for conservation despite their high biodiversity. If intensely developed lowland areas with high flooding risk overlap with important sites for biodiversity conservation, it would be reasonable to try to harmonize biodiversity conservation and human development in human‐inhabited lowland areas. Here, we examined whether extant PAs can conserve macroinvertebrate and freshwater fish biodiversity and whether human‐inhabited lowland flood risk management sites might be suitable to designate as freshwater protected areas (FPAs).LocationAcross Japan.MethodsWe examined whether extant PAs can conserve macroinvertebrate and freshwater fish biodiversity and analysed the relationship between candidate sites for new FPAs and flood disaster risk and land use intensity at a national scale across Japan based on distribution data for 131 freshwater fish species and 1395 macroinvertebrate species.ResultsWe found that extant PAs overlapped with approximately 30% of conservation‐priority grid cells (1 km2) for both taxa. Particularly for red‐listed species, only one species of freshwater fish and three species of macroinvertebrate achieved the representation target within extant PAs. Moreover, more than 40% of candidate conservation‐priority grid cells were located in flood risk and human‐occupied areas for both taxa.Main conclusionsFloodplain conservation provides suitable habitat for many freshwater organisms and helps control floodwaters, so establishing new FPAs in areas with high flood risk could be a win‐win strategy for conserving freshwater biodiversity and enhancing ecosystem‐based DRR (eco‐DRR).