Sea-level reconstructions over the past two millennia provide a pre-industrial context to assess whether the magnitude and rate of modern sea-level change is unprecedented. Sea-level records from the Indian Ocean over the past 2,000 years are sparse, while records from the Atlantic and Pacific Oceans show variations less than 0.25 m and no significant negative excursions. Here, we present evidence of two low sea-level phases in the Maldives, Indian Ocean, based on fossil coral microatolls. Microatoll growth is constrained by low water levels and, consequently, they are robust recorders of past sea level. U–Th dating of the Maldivian corals identified lowstands at AD 234–605 and AD 1481–1807 when sea level fell to maximum depths of −0.88 m and −0.89 m respectively. These lowstands are synchronous with reductions in radiative forcing and sea surface temperature associated with the Late Antiquity Little Ice Age and the Little Ice Age. Our results provide high-fidelity observations of lower sea levels during these cool periods and show rates of change of up to 4.24 mm yr−1. Our data also confirm the acceleration of relative sea-level rise over the past two centuries and suggest that the current magnitude and rate of sea-level rise is not unprecedented.