We present CTD and ADCP surveys around the Indian Ocean coral atolls of Aldabra (46°20′E, 9°25′S) and Cosmoledo (47°30E, 9°45′S) during April–July 1987. These isolated, steep-sided islands situated in deep (4000 m) water in the South Equatorial Current provide examples of flow disturbance which are compared to laboratory studies of eddy generation by a circular cylinder in a channel. For sufficiently strong and steady flows, a doming of the isopycnals is observed in the lee of the islands. The sea-surface temperature decreases and the salinity increases as cool, saline water is mixed from below. Just as in the case of islands in tidally dominated shelf seas, we observe an increase in the chlorophyll content of the water behind the island, indicative of enhanced phytoplankton productivity caused by the flow disturbance. This anomalous region may be associated with an eddy trapped downstream of the island. The incident flows were not strong enough to generate a vortex street of eddies spun off in a wake. When the incident flows are weak and fluctuating, no evidence for eddies is seen; and there is no doming of the isopycnals leading to low sea-surface temperature and high chlorophyll content.