Chilean fjord sediments constitute high-resolution archives of climate and environmental change in the southern Andes. To interpret such records accurately, it is crucial to understand how sediment is transported and deposited within these basins. This issue is of particular importance in glaciofluvial Martínez Channel and Steffen Fjord (48°S), due to the increasing occurrence of Glacial Lake Outburst Floods (GLOFs) originating from outlet glaciers of the Northern Patagonian Icefield. Hence, the bathymetry of the head of Martínez Channel and Steffen Fjord was mapped at high resolution and the grain-size and organic carbon content of grab sediment samples were examined. Results show that the subaquatic deltas of Baker and Huemules rivers at the head of Martínez Channel and Steffen Fjord, respectively, are deeply incised (up to 36 m) by sinuous channels. The presence of sediment waves and coarser sediments within these channels imply recent activity and sediment transport by turbidity currents. Although several triggering mechanisms are possible, we argue that elevated river discharge and the associated relatively high suspended sediment loads is the main cause of the occurrence of turbidity currents at the head of these fjords and are of key importance in shaping the fjord's subaquatic morphology. This study shows that the heads of Martínez Channel and Steffen Fjord are dynamic sedimentary environments with rapidly migrating channels. It highlights the importance of site selection and multi-coring in any future project aimed at reconstructing environmental change using the sediments of either fjord.