Global sea level has risen during the past decades as a result of thermal expansion of the warming ocean and freshwater addition from melting continental ice. However, sea-level rise is not globally uniform. Regional sea levels can be affected by changes in atmospheric or oceanic circulation. As long-term observational records are scarce, regional changes in sea level in the Indian Ocean are poorly constrained. Yet estimates of future sea-level changes are essential for effective risk assessment. Here we combine in situ and satellite observations of Indian Ocean sea level with climate-model simulations, to identify a distinct spatial pattern of sea-level rise since the 1960s. We find that sea level has decreased substantially in the south tropical Indian Ocean whereas it has increased elsewhere. This pattern is driven by changing surface winds associated with a combined invigoration of the Indian Ocean Hadley and Walker cells, patterns of atmospheric overturning circulation in the north-south and east-west direction, respectively, which is partly attributable to rising levels of atmospheric greenhouse gases. We conclude that-if ongoing anthropogenic warming dominates natural variability-the pattern we detected is likely to persist and to increase the environmental stress on some coasts and islands in the Indian Ocean.