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Ecosystems are intrinsically linked, such that management actions in one ecosystem can influence adjacent ecosystems. However, adequate data, and even protocols, for monitoring cross-ecosystem responses to conservation initiatives are lacking. Here, we evaluate potential indicators, operating on different spatial, temporal, and biological scales, for measuring the effects of island-based restoration on coral reef ecosystems. We show that island restoration status had consistent effects on populations of tropical seabirds across spatial scales from 100 m to entire islands. Seabirds, in turn, provided nutrient subsidies that were incorporated by marine algae and coral-reef fishes, with the most pronounced effects closer to shore, at leeward sites, and at low trophic levels. Microbes and macroalgae exhibited assemblage-level responses to seabird-derived nutrients entering the marine environment, but there were few differences in coral reef benthic and fish assemblages. By identifying and focusing on specific indicators such as macroalgal nutrients, managers can better monitor cross-ecosystem responses to conservation interventions with limited resources.