Measurements of 231 Pa, 230 Th and 232 Th concentrations have been made on five water-column profiles along the western margin of the Madagascar and Mascarene Basins in the southern Indian Ocean. These measurements help to fill a significant gap in the global coverage of water-column 232 Th, 230 Th and 231 Pa data. 232 Th concentrations vary, but generally increase with depth, suggesting higher particle loading in deeper waters, and the presence of a significant dissolved fraction of 232 Th. 230 Th concentrations increase with depth, and profiles are similar to the average of existing data from other regions. 231 Pa concentrations, on the other hand, show significant depth structure, apparently reflecting the various water masses sampled at this location. The modified remnants of North Atlantic Deep Water are found at a depth of 62000 m and exhibit elevated 231 Pa concentrations exported from the South Atlantic. Antarctic Intermediate and Bottom Waters have lower 231 Pa, probably due to scavenging onto opal particles during transit from the Southern Ocean. The differences between water masses raises a question: which water mass is important in controlling the 231 Pa/ 230 Th ratio in underlying sediments? A simple one-dimensional model is used to demonstrate that the 230 Th and 231 Pa exported to sea-floor sediments last equilibrates with waters close to the seafloor (within 61000 m), rather than averaging the whole water column. These findings suggest that 231 Paxs/ 230 Thxs in sediments provides information primarily about deep-water masses. In this region, sedimentary records will therefore provide information about the past flow of Antarctic Bottom Water into the Indian Ocean. Interpretation of data from other regions, such as the North Atlantic where this proxy has most successfully been applied, requires careful consideration of regional oceanography and knowledge of the composition of the water masses being investigated. D 2005 Elsevier B.V. All rights reserved.