The hydrography of the Arctic Seas is being altered by ongoing climate change, with knock-on effects to nutrient dynamics and primary production. As the major pathway of exchange between the Arctic and the Atlantic, the Fram Strait hosts two distinct water masses in the upper water column, northward flowing warm and saline Atlantic Waters in the east, and southward flowing cold and fresh Polar Surface Water in the west. Here, we assess how physical processes control nutrient dynamics in the Fram Strait using nitrogen isotope data collected during 2016 and 2018. In Atlantic Waters, a weakly stratified water column and a shallow nitracline reduce nitrogen limitation. To the west, in Polar Surface Water, nitrogen limitation is greater because stronger stratification inhibits nutrient resupply from deeper water and lateral nitrate supply from central Arctic waters is low. A historical hindcast simulation of ocean biogeochemistry from 1970 to 2019 corroborates these findings and highlights a strong link between nitrate supply to Atlantic Waters and the depth of winter mixing, which shoaled during the simulation in response to a local reduction in sea-ice formation. Overall, we find that while the eastern Fram Strait currently experiences seasonal nutrient replenishment and high primary production, the loss of winter sea ice and continued atmospheric warming has the potential to inhibit deep winter mixing and limit primary production in the future.