In mountainous terrain, the relationship between ice sheet dynamics and basal topography is complex, with each component influencing the other. This paper investigates how the last glacial maximum Antarctic Peninsula Ice Sheet might have modified its bed both at maximum extent and during progressive grounding line retreat. Focussing on the Marguerite Trough Ice Stream we then examine the degree to which basal topographical conditions affected the rate of ocean-forced recession. Zones of peak subglacial erosion are preferentially located in areas of convergent flow and where horizontal strain rates are highest. During ice sheet retreat, potential erosion rates increase in these areas, but the foci remain fixed. This leads to selective and progressive deepening of subglacial basins. As grounding lines migrate landward, faster retreat tends to occur over subglacial basins, especially if flow is divergent, whereas slower retreat takes place on sloping beds and where the geometry of the outlet allows convergent flow and a non-negative flux balance. In conclusion the Antarctic Peninsula Ice Sheet selectively erodes its bed beneath linear outlets and, over successive glacial cycles, progressive deepening of subglacial basins may bring about non-linear retreat of the ice sheet margin.