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Glacier and ice sheet mass loss as a result of climate change is driving important coastal changes in Arctic fjords. Yet limited information exists for Arctic coasts regarding the influence of glacial erosion and ice mass loss on the occurrence and character of turbidity currents in fjords, which themselves affect delta dynamics. Here we show how glacial erosion and the production of meltwaters and sediments associated with the melting of retreating glaciers control the generation of turbidity currents in fjords of eastern Baffin Island (Canada). The subaqueous parts of 31 river mouths along eastern Baffin Island were mapped by high-resolution swath bathymetry in order to assess the presence or absence of sediment waves formed by turbidity currents on delta fronts. By extracting glaciological and hydrological watershed characteristics of these river mouths, we demonstrate that the presence and areal extent of glaciers are a key control for generating turbidity currents in fjords. However, lakes formed upstream during glacial retreat significantly alter the course of sediment routing to the deltas by forming temporary sinks, leading to the cessation of turbidity currents in the fjords. Due to the different deglaciation stages of watersheds in eastern Baffin Island, we put these results into a temporal framework of watershed deglaciation to demonstrate how the retreat pattern of glaciers, through the formation and filling of proglacial lakes, affects the turbidity current activity of deltas.