Subglacial discharge from marine-terminating glaciers in Greenland injects large volumes of freshwater and suspended sediment into adjacent fjord environments. Although the discharge itself is nutrient poor, the formation of meltwater plumes can enhance marine biological production by stimulating upwelling of nutrient-rich fjord water. Despite the importance of meltwater discharge to marine ecosystems, little is known of the quantitative impact of discharge processes on phytoplankton growth, including the effects of local plumes, fjord-wide stirring and mixing, and suspended sediments on net primary production (NPP). Here, we report simulations of Bowdoin Fjord in northwestern Greenland using coupled non-hydrostatic ocean circulation and lower-trophic level ecosystem models, developed using field data. Our findings demonstrate that subglacial discharge plays a crucial role in NPP by stirring and mixing the entire fjord water system, which has a greater effect on NPP than local plume upwelling. Sensitivity tests suggest a 20% increase in NPP under conditions of enhanced discharge anticipated in the future. However, if glacier discharge and retreat exceed critical levels, NPP is predicted to decline by 88% relative to present values. This pattern reflects the negative impact of increased sediment flux on photosynthesis and weakened fjord stirring and mixing resulting from shallower outlet depths.