Radar altimetry provides sea ice thickness estimates for polar region. However, uncertainty in the scattering horizon used to retrieve sea ice thickness arises from interactions between the emitted signal and snow cover on the ice surface. Therefore, improving our knowledge on electromagnetic waves scattering with the snowpack and ice is necessary to retrieve sea ice thickness accurately. The Snow Microwave Radiative Transfer (SMRT) model was used to simulate the low-resolution altimeter waveform echo from snow-covered sea ice, using in-situ measurements as input. In-situ measurements from four field campaigns in three distinct Canadian Arctic regions includes temperature, salinity, density, specific surface area, microstructure from X-ray tomography and surface roughness measurements using structure from motion photogrammetry. Evaluation of SMRT in altimeter mode was performed against CryoSat-2 waveform data in pseudo-low-resolution mode. Simulated and observed waveforms showed good agreement, although it was necessary to optimize the snow and sea ice roughness. In addition, simulations of backscatter in low-resolution mode in preparation for the European Space Agency’s CRISTAL mission indicated that the dominant return comes from the ice surface at Ku-band and from the snow surface at Ka-band for smooth first-year ice. However, for rougher multi-year ice, the main scattering comes from the snow surface for both Ku and Ka-band. These findings depend on the parameterisation of the roughness. This work offers insight into the dominant surface return for Ku and Ka and paves the way towards a physical retracker using SMRT to retrieve snow depth and sea ice thickness for radar altimeter missions.