Sea-level rise drives the redistribution of coastal ecosystems. Ecosystems are linked within landscapes by the physical and biological processes they mediate. In connected landscapes, the response of one ecosystem to sea-level rise could have influence neighbouring systems. In shallow tropical coastal marine ecosystems, coral reefs shelter lagoons from incoming waves allowing seagrass meadows to thrive in lagoons. Deepening water over coral reefs from sea-level rise allows larger, more energetic waves to traverse into the lagoon, deteriorating conditions for seagrass. Coral reef growth to maintain relative water depth could potentially mitigate negative effects of sea-level rise on seagrass. We conducted an interdisciplinary field and modelling study at Lizard Island, Great Barrier Reef, where shallow seagrass meadows thrive inshore of a barrier reef. We predict negative effects of sea-level rise on seagrass before mid-century under moderate to high greenhouse gas emissions scenarios and given reasonable rates of reef growth. This is because rates of vertical carbonate accretion typical of modern reef flats, up to 3 mm·yr^-1, appear insufficient to maintain suitable conditions for reef seagrass. This is the first quantitative prediction of interdependencies between ecosystems in response to climate change. The results highlight the need for landscape scale management plans which consider the interdependent responses of multiple ecosystems to climate change.