Coastal eutrophication is an issue of serious global concern and although nutrient subsidies can enhance primary productivity of coastal wetlands, they can be detrimental to their long-term maintenance. By supplying nutrients to coastal ecosystems at levels comparable to intensive agriculture practices, roosting colonial waterbirds provide a natural experimental design to examine the impacts of anthropogenic nutrient enrichment in these systems. We tested the hypothesis that long-term nutrient enrichment from bird guano deposition is linked to declines in island size, which may subsequently decrease the stability and resilience of mangrove cays in Belize. We combined remote sensing analysis with field- and lab-based measurements of forest structure, sediment nutrients, and porewater nutrients on three pairs of rookery and control cays in northern, central, and southern Belize. Our results indicate that rookery cays are disappearing approximately 13 times faster than cays without seasonal or resident seabird populations. Rookery cays were associated with a significantly higher concentration of nitrogen (N) in mangrove leaves and greater aboveground biomass, suggesting that eutrophication from bird guano contributes to increased aboveground productivity. Sediments of rookery cays also had lower percentages of soil organic matter and total N and carbon (C) than control islands, which suggests that eutrophication accelerates organic matter decomposition resulting in lower total C stocks on rookery cays. Our results indicate that coastal eutrophication can reduce ecosystem stability by contributing to accelerated cay loss, with potential consequences for mangrove resilience to environmental variability under contemporary and future climatic scenarios.