Increased ocean‐to‐ice heat fluxes play a key role in the accelerated mass loss of Greenland’s marine‐terminating glaciers. Ocean current variability leads to variations in this heat flux. A year‐long time series of ocean currents at all gateways to the ocean cavity under Greenland’s largest remaining floating ice tongue at the Nioghalvfjerdsfjorden Glacier (79NG) was analyzed. The variability of the exchange flow at intra‐annual to near‐daily timescales was characterized. The currents exhibit considerable variability with standard deviations exceeding the time mean flow strength by a factor of 2. The inflow of warm Atlantic Intermediate Water into the cavity and the outflow via the northernmost calving front were directly coupled on intra‐annual timescales (periods, T > 30 days) with enhanced fluctuations in the winter months. A strong correlation between the variability of the deep inflow and currents in the subsurface boundary current on the continental shelf suggests a link between cavity and continental shelf circulation. Variability on higher frequencies (T < 30 days) in the outflow was only partly induced by the inflow variability. Two export branches of the cavity circulation were identified, which were potentially constrained by subglacial meltwater channels. The relative importance of the two export branches varies on monthly time scales. This research has provided evidence that the large intra‐annual ocean current variability at the 79NG is strongly influenced by the continental shelf circulation. Temporally varying preferred export routes increase the complexity of the cavity circulation.