Measurements of Pa-231, Th-230 and Th-232 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 Th-232, Th-230 and Pa-231 data. Th-232 concentrations vary, but generally increase with depth, suggesting higher particle loading in deeper waters, and the presence of a significant dissolved fraction of Th-232. Th-230 concentrations increase with depth, and profiles are similar to the average of existing data from other regions. Pa-232 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 approximate to 2000 in and exhibit elevated Pa-231 concentrations exported from the South Atlantic. Antarctic Intermediate and Bottom Waters have lower Pa-231, 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/Th-230 ratio in underlying sediments? A simple one-dimensional model is used to demonstrate that the Th-230 and Pa-231 exported to sea-floor sediments last equilibrates with waters close to the seafloor (within approximate to 1000 in), rather than averaging the whole water column. These findings suggest that Pa-231(xs)/Th-230(xs) 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. (c) 2005 Elsevier B.V All rights reserved.