Submarine basal melt of the Greenland Ice Sheet remains a major uncertainty in climate ice-sheet modelling and projections of future sea level rise. In lieu of sufficient observations, development of robust basal melt parameterizations relies on high resolution ocean models of glacial fjords quantifying oceanic thermal forcing for given ice and fjord geometry,  stratification and forcing, and exploring ocean warming scenarios. As Greenlandic fjords are typically narrower than the length scale for which the Earth's rotation would affect the circulation and oceanic heat flux towards the ice, ocean models often employ a two-dimensional configuration for computational efficiency. Here we show that the interplay of ice and fjord geometry, stratification and friction makes the circulation in ice cavity three-dimensional and affected by Earth's rotation even in narrow fjords, with fivefold effect on the average basal melt in our simulations. Our study prompts using three-dimensional model configurations of Greenlandic fjords as well as focused observational campaigns to quantify the multiple factors missing in two-dimensional simulations.