In 1987, conductivity-temperature-depth and current data were collected in two oceanographic surveys carried out around the Indian Ocean coral atolls of Aldabra (46° 20′ E, 9° 25′ S) and Cosmoledo (47° 30′ E, 9° 45′ S) between April and July. During the surveys, significant changes were observed in the temperature and salinity of the upper layers. From temperature-salinity analysis, the dominant water masses in the upper layers (0–400 m) were categorized and their origin determined. During the first cruise, TS characteristics changed only slightly. Low salinity waters (S = 34.5–34.6 and T = 28°–30°C), brought from the east by the South Equatorial Current, were dominant in the surface layers. During the second cruise, the surface waters were saltier and cooler (S = 35.1 and T = 25°–26°C) and more homogeneous in the upper 200 m as a result of a greater admixture of a southern water mass. Seasonal cooling at this time was responsible for a deeper surface mixed layer. Near the end of the cruise, TS conditions changed suddenly due to an invasion of southern subtropical water masses in the layers above 200 m. Current meter records were dominated by the regional 50-day oscillation and higher-frequency variability and did not show the expected increase in strength of the South Equatorial Current to indicate onset of the southwest monsoon. The water mass changes were not correlated with changes in the local currents and were probably caused by advection of patches by the large-scale flow.