A 27 m core collected on the seafloor near Juan de Nova island at 1909 m depth in the SW Indian Ocean preserves a high‐resolution record of carbonate sediment export to the deep sea over the past 1 Myr. Core chronology was established using calcareous nannofossil biostratigraphy and benthic foraminiferal δ18O. Throughout the core, preserved highstand intervals (MIS 1, 5, 7, 9, 11, 13, 15, 23 and 25) are marked by an increase in the aragonite content within the sediment. Aragonite is likely sourced from the nearby Juan de Nova carbonate platform ~10 km to the south, and is interpreted to result from flooding of the platform top. Platform inundation allows carbonate muds to be winnowed from their original shallow‐water environment of deposition, suspended in the water column, and redeposited onto the proximal slopes and within the basin. Sharp increases in aragonite content at the beginning of each highstand interval can be used to estimate the approximate sea‐level range when platform flooding occurred; results show that the depth of the platform top has likely changed little over the past 1 Myr due to balanced aggradation and subsidence. Previously hypothesized large‐scale aragonite dissolution cycles are evidenced by a disproportionally low aragonite increase during MIS 11. This study provides a new, exceptionally long record of highstand shedding, expanding the known occurrences of the process to the southern Indian Ocean and supporting its importance as a globally significant depositional mechanism that impacts deep‐sea stratigraphic records.