Cross-ecosystem nutrient fluxes can influence recipient food webs, including both static measures of structure and dynamic measures of function. However, a mechanistic basis for how nutrient subsidies affect both structure and function across multiple trophic levels is still lacking. Here, we investigate how nutrient subsidies provided by seabirds influence coral reefs, focusing on the link between primary producers and primary consumers. We quantified turf algal cover and herbivorous fish biomass (static metrics of structure), as well as productivity of turf algae and herbivorous fish (dynamic metrics of function) at sites in the inner Seychelles with a range of seabird densities due to different rat invasion histories. Turf algae grew faster with increasing amounts of seabird-derived nutrients. These higher rates of primary productivity, in turn, fueled higher productivity and biomass of herbivorous fishes. In contrast, seabird-derived nutrients did not increase cover of turf algae nor did turf algal cover affect herbivores. Instead, seabird nutrients indirectly enhanced herbivorous fish productivity and biomass via effects on primary productivity, which, in turn, led to increased top-down control by herbivores to limit turf algal cover. Overall, dynamic metrics better revealed the flow and effects of seabird-derived nutrients through coral-reef food chains and revealed the mechanisms by which seabirds can enhance coral-reef ecosystem function. These findings could be used to predict the benefits of removing introduced rats from islands, which can increase seabird populations and restore nutrient connectivity, thus potentially enhancing ecosystem function across multiple trophic levels on coral reefs.