Predicted sea-level rise and increased storm frequency caused by climate change drastically threaten low-lying inhabited coral atolls. Coral reef frameworks are the atolls' primary defence from these changes. The growth and integrity of these frameworks is reflected in their carbonate budgets, a dynamic balance between biogenic accretion through coral growth and erosional forces, both of which are affected by factors acting at different spatial scales. We explored how carbonate budgets, estimated using the ReefBudget methodology, vary between three inhabited atolls that face differing anthropogenic stressors in the Lakshadweep Archipelago in the Northern Indian Ocean. We surveyed ten reefs, at two depths each, across the three islands. Overall, net carbonate budgets of reefs across all atolls were below optimal production rates needed to continue protecting shorelines (5 G measured on healthy reefs). This was a result of repeated mass bleaching events as well as local impacts. Carbonate production was influenced by a recent mass bleaching event in 2016 and a cyclone in 2018, and varied between depths and exposures, potentially due to differential recovery and mortality dynamics. Erosional processes were locally mediated with both urchin and parrotfish density showing large differences between islands, possibly linked to nutrient outflow and fishing intensity. We also find that by the year 2100, a large proportion of shallow sites will experience an increase in water depth above half a metre under moderate and high emissions scenarios, but none will breach this threshold under a low emissions scenario. Our results show that patterns of carbonate production were largely mediated by the history of global/regional disturbances, while erosional rates were much more dependent on local factors.