One of the key sources of uncertainties in sea ice freeboard and thickness estimates derived from satellite radar altimetry results from changes in sea ice surface properties. In this study, we analyse this effect, comparing upward-looking sonar (ULS) measurements in the Beaufort Sea over the period 2003–2018 to sea ice draft derived from Envisat and Cryosat-2 data. We show that the sea ice draft growth underestimation observed for the most of winter seasons depends on the surface properties preconditioned by the melt intensity during the preceding summer. The comparison of sea ice draft time series in the Cryosat-2 era indicates that applying 50% retracker thresholds, used to produce the European Space Agency’s Climate Change Initiative (CCI) product, provide better agreement between satellite retrievals and ULS data than the 80% threshold that is closer to the expected physical waveform interpretation. Our results, therefore, indicate compensating error contributions in the full end-to-end sea-ice thickness processing chain, which prevents the quantification of individual factors with sea-ice thickness/draft validation data alone