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Cross-ecosystem nutrient transfer can enhance coral reef functioning in an otherwise oligotrophic environment. While the influence of seabird-derived nutrients on coral reef organisms is increasingly recognized, how they are integrated into reef food webs remains unclear. Cryptobenthic reef fishes are crucial for energy transfer on coral reefs, and their fast life histories imply that they respond strongly to seabird-derived nutrients. Here, we investigate how variation in nearshore seabird nutrient subsidies affects coral reef fish communities. By comparing fish communities across locations differing in seabird nutrient inputs and using stable isotope analysis, we explore nutrient integration across depth, their influence on cryptobenthic and associated larger reef fishes and investigated the relative reliance of cryptobenthic fishes on seabird-enriched benthic and non-enriched pelagic pathways. We find that, near seabird colonies, cryptobenthic fishes’ diets can transition from pelagic to benthic dominance; cryptobenthic fish communities are larger; herbivores and all feeding groups comprising potential cryptobenthic fish predators have higher biomass. Collectively, our results stress the importance of seabirds in shaping energy pathways and suggest that, even in dynamic, ocean-swept reef systems, cryptobenthic fishes can mobilize seabird subsidies and potentially act as a nutritional bridge to higher trophic levels.