We present Nd isotopic data for fossil fish teeth recovered from the past 40 m.y. at ODP Site 757, currently located at 1650 m water depth on the Ninetyeast Ridge in the Indian Ocean. Although Site 757 sits in a region strongly influenced by weathering inputs from the Himalayas and volcanic inputs from the Indonesian arc, the pattern of Nd isotopic variations does not appear to respond to these potential sources of Nd. Instead, secular variations correlate to changes in the composition of intermediate to deep water masses bathing the site and circulation patterns in the Indian Ocean. From ∼40 to 10 Ma, ɛNd values and the pattern of change at Site 757 closely match those of ODP Site 1090, a deep water site in the Atlantic sector of the Southern Ocean. Comparison to data from several Fe-Mn crusts in the Indian Ocean suggests that intermediate to deep water flow paths were similar to the modern distribution of Circumpolar Deep Water. At approximately 10 Ma, Nd isotopic values increase in a step function by 2 ɛNd units, suggesting that plate motions had carried Site 757 into a region influenced by Indonesian Throughflow. Estimates of the vertical and horizontal position of this site at 10 Ma imply that Indonesian Throughflow extended as far south as ∼20°S and to a depth of ∼1500 m. From 10 to 0 Ma, Nd isotopic variations at Site 757 appear to record variations in Indonesian Throughflow. From 10 to 5.5 Ma, values at Site 757 overlap with those from crusts located in the southwest Pacific, indicating extensive flow through the Indonesian Seaway. From 5.5 to 3.4 Ma, ɛNd values become less radiogenic at Site 757 and more radiogenic in the southwest Pacific, suggesting increasing closure of the seaway and concomitant rerouting of equatorial Pacific waters. Beginning at 3.4 Ma, ɛNd values become more radiogenic again at Site 757, which may be attributed to enhanced opening of the seaway or to a change in the source of Throughflow waters from a southern to a northern Pacific region.