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Despite major advances in quantifying species vulnerability and threats, we still lack a crucial understanding of where threats are affecting freshwater species globally. Here, we produced a species-centered spatial assessment of threats, mapping the impact of 45 threats across 21,490 freshwater species of amphibians, fish, mammals, odonates, and reptiles. We found that species in highly developed and water-managed regions are strongly affected by multiple overlapping threats. Although threats vary across taxa and regions, increasing threat probabilities elevate extinction risk and population declines, with freshwater species experiencing greater threat intensity and distinct spatial patterns than terrestrial species. 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