Changes in firn properties affect the shape of pulse-limited radar altimeter echoes acquired over the polar ice sheets. We apply a waveform deconvolution model to CryoSat-2 low-resolution mode echoes to determine the depth distribution of radar backscattering across the Greenland Ice Sheet. The deconvolution allows us to calculate the relative contributions of surface and volume scattering and the effective penetration depth of the radar echoes into the snowpack. The most prominent signal is associated with the extreme surface melting of summer 2012, which resulted in a shift of the dominant radar scattering horizon toward the snow surface in the accumulation zone. At locations above 2000 m, the average penetration depth in July 2012 (prior to the melt event) was 3.79 ± 1.12 m. Following the melt event, there was an abrupt reduction in the average penetration depth across the same region to 1.45 ± 0.94 m. The average penetration depth then gradually increased to 3.28 ± 1.13 m by the end of 2017, as fresh snow accumulated on the ice sheet surface. Although the variation in penetration is evident in surface height estimates derived from the CryoSat-2 echoes, the magnitude of the effect is reduced by waveform retracking. Using airborne laser altimeter data recorded over the same time period, we show that the penetration variation can be compensated effectively by incorporating the deconvolution penetration depth into the surface height retrieval.