Human exploitation has profoundly depleted animal populations in the ocean, leading to declines in ecosystem productivity, resilience, and contributions to people1,2. However, it remains unclear how size structure of fish populations varies across marine habitat and levels of human exploitation while simultaneously underpinning food web architecture and ecosystem functioning3. Here, we process 6,701 pelagic and 10,710 benthic stereo-video deployments across all the oceans to extract body size of over 800,000 individual fish, spanning 6 orders of magnitude from zooplankton size-classes (<1 g), to large oceanic predators (>1,000 kg), in order to ultimately assess vulnerability to exploitation and responses to protection status. Size-spectra analysis reveals peaks in body size distributions which differ in their position between pelagic and benthic habitats. Typical body size of relatively small and large individuals is greater in strictly protected areas remote from human markets, than in unprotected areas close to markets. Pelagic size-spectra are more sensitive to market remoteness and respond more strongly to protection than their benthic counterparts which are more species-rich, and therefore more likely to provide trophic replacements4 under exploitation, owing to body size redundancy5. This contrasted result suggests that fully protected areas can partly mitigate human impacts close to markets in benthic habitats while in pelagic habitats effective protection requires remoteness from humans. Thus, the restoration of fish body-size spectra, including some of the world’s largest and most endangered vertebrates6, can be promoted by implementing fully protected areas in pelagic habitats, particularly in remote locations.