Seismic reflection data from the southern Mozambique Ridge, Southwestern Indian Ocean, show indications for a substantial modification in the oceanic circulation system during the Neogene. Major reorganisations in the Indian Ocean circulation system accompanying the closure of the Indonesian Gateway led to the onset of current controlled sedimentation in the vicinity of the Mozambique Ridge at ~14 million years ago. The modifications in water mass properties and pathways are documented in changes in reflection characteristics in the Mozambique Ridge area. The evidence from the seismic reflection data is compared to deep water Pb, Nd and Hf isotope time series of the past 20 million years obtained from three hydrogenetic ferromanganese crusts and one manganese nodule from the Mozambique Ridge in the SW Indian Ocean. The isotope systems enable tracing of the source provenances of deep water masses. The ferromanganese precipitates were recovered from 1850 m, 2780 m and 3790 m water depth and were dated by cosmogenic 10Be/9Be profiles. These precipitates serve as unique archives of the long term evolution of the mixing of ambient Indian Ocean water masses ultimately originating from the North Atlantic and the Southern Ocean at the respective depths over time. The evolution of the admixture of North Atlantic Deep Water at water depths greater than 2000 m is clearly mirrored by Nd and Hf isotopic compositions systematically about one ε unit lower than those of the overlying Antarctic Intermediate Water. This stratification has only existed since 9 million years ago suggesting that the general present day large scale circulation in the intermediate and deep southern Indian Ocean has only prevailed since then.