Mixed turbidite-contourite systems can be found in oceans where bottom currents and turbidity currents interact. The Zambezi turbidite system, located in the Mozambique Channel (SW Indian Ocean), is one of the largest sedimentary systems in the world in length and area of the related catchments. The oceanic circulation in the Mozambique Channel is intense and complex, dominated by eddies flowing southwards and deep currents flowing northwards along the Mozambican margin. Current measurements obtained from moorings at 3400–4050 m water depth in the Zambezi and Tsiribihina valleys show periods of intense currents at the seafloor with peaks of 40–50 cm s−1 that last up to one month and are not related to turbidity currents. These strong bottom-current events are correlated with a change in current direction and an increase in temperature. The periods of current intensification may be related to eddies, since they present similar frequencies (around 7 per year). Moreover, modelling results show that during periods of intense deep circulation an anticyclonic eddy is present between the Mozambican slope and the centre of the Mozambique Channel, which may block the northward transport of the deep water mass and thus enhance the southward transport along the western slope of Madagascar. According to our hydrodynamic modelling of the circulation near the seafloor, intense currents are often present along the Zambezi Valley, especially along the valley flanks. Multi-channel seismic reflection data show that the Zambezi turbidite system does not show the typical characteristics of turbidite systems, being dominated by erosional processes, which mainly affect the valley flanks. Levees associated with the valley are absent in the main axis of the system. The effect of bottom currents on sedimentation in the basin is evidenced by the low sedimentation rates that witness winnowing in the basin, the presence of contouritic sand in the Zambezi Valley flanks and the abundance of current-related bedforms observed in multibeam bathymetry and seismic data. The intense oceanic processes observed in the Mozambique Channel may transport a large part of the fine sediment out of the basin and erode the seafloor even at great depths. Therefore, the Zambezi turbidite system could at present be considered as a mixed turbidite-contourite system, with important implications for source-to-sink studies.