The Institute Ice Stream (IIS) rests on a reverse-sloping bed, extending >150 km upstream into the ~1.8 km deep Robin Subglacial Basin, placing it at the threshold of marine ice-sheet instability. Understanding IIS vulnerability has focused on the effect of grounding-line melting, which is forecast to increase significantly this century. Changes to ice-flow dynamics are also important to IIS stability, yet little is known about them. Here we reveal the trunk of the IIS occurs downstream of the intersection of three discrete subglacial features; a large ‘active’ subglacial lake, a newly-discovered sharp transition to a zone of weak basal sediments, and a major tectonic rift. The border of IIS trunk flow is confined by the sediment on one side, and by a transition between basal melting and freezing at the border with the Bungenstock Ice Rise. By showing how basal sediment and water dictate present-day flow of IIS, we reveal that ice-sheet stability here is dependent on this unusual arrangement.