The West Antarctic Rift System is one of the least understood rift systems on earth, but displays a unique coupled relationship between tectonic processes and ice sheet dynamics. Geothermal heat flux is a poorly constrained parameter in Antarctica and suspected to affect basal conditions of ice sheets, i.e., basal melting and subglacial hydrology. Thermomechanical models demonstrate the influential boundary condition of geothermal heat flux for (paleo-)ice sheet stability. Young, continental rift systems are regions with significantly elevated geothermal heat flux, because the transient thermal perturbation to the lithosphere caused by rifting requires ~100 Ma to reach long-term thermal equilibrium. We discuss airborne, high-resolution magnetic anomaly data from the Amundsen Sea sector to provide additional insight into deeper crustal structures related to the West Antarctic Rift System in the Amundsen Sea sector. Using depth-to-the-bottom of the magnetic source (DBMS) estimates, we reveal spatial changes at the bottom of the igneous crust and the thickness of the magnetic layer, which can be further incorporated into tectonic interpretations and which is used to derive geothermal heat flux, supplemented by heat flux derived from measured temperature gradients in shelf sediments. We relate the distribution of geothermal heat flux to paleo and present ice sheet flow conditions.