Coral reefs receive both passive and active nutrient subsidies, supplied via oceanographic processes and animal-mediated transfer, which can bolster reef productivity and resilience to disturbance. We examined the relative importance of these two pathways across lagoonal and seaward reefs, reefs of different depths, and those around islands either with or without breeding seabird colonies using carbon and nitrogen stable isotopes (ð13C and ð15N) and nutrient metrics (per cent N, %N and carbon-to-nitrogen ratios, C:N). We found increased passive oceanic nutrient inputs in reefs that were both deep and seaward facing, indicated by lower ð13C values. Enriched ð15N values and lower carbon-to-nitrogen ratios within reefs adjacent to islands with seabird colonies provided evidence of the role of seabirds as active vectors of nutrients to coral reef food webs, particularly within shallow, lagoonal reefs. Though %N values did not seem to provide a good indicator through which to disentangle active vs passive nutrient transport within this context, variation in ð13C and ð15N values and C:N ratios highlighted the interplay between passive oceanic processes and active seabird contributions to coral reefs. We emphasise the importance of both preserving and restoring natural nutrient pathways, particularly at a time when coral reef ecosystems are under increasing pressure from anthropogenic threats.