Abstract The bedrock beneath the Antarctic Ice Sheet has experienced widespread viscoelastic deformation as a response to ice-sheet changes from the Last Glacial Maximum (LGM) to present day. The combined changes of the ice sheet and the bedrock most likely had impacted subglacial water routes. Using the evolution of bedrock elevation simulated with two coupled ice-sheet and glacial isostatic adjustment (GIA) models, we explore changes to the subglacial water routes from the LGM to the present day. We explore the sensitivity of our results to bed roughness by repeating the calculations using 10 topographic realizations, and estimate the relative impacts of changes in the bedrock elevation and the ice surface slope. Our results show that bedrock elevation changes of up to ∼400 m likely led to a large enough change in tilt of the bedrock, such that subglacial water routing during the last deglacial phase likely differed significantly from patterns inferred at present day. The impact of GIA on subglacial flow paths is thus non-negligible and should be accounted for in reconstructions of ancient subglacial hydrology and studies of past sediment provenance.