Abstract The Surface Water and Ocean Topography (SWOT) mission promises quasi‐global monitoring of glacial lakes, yet the elevation difference arising from its Ka‐band radar penetrating lake snow/ice cover remains unquantified. This poses a challenge to assessing their level changes. We present the first quantification of this difference by intercomparing SWOT and ICESat‐2 surface elevations over 260 glacial lakes (>1 km2) globally. Given ICESat‐2’s laser measures the snow/ice surface, we leverage near‐synchronous observations to treat the elevation difference as an empirical measure of the snow/ice penetration effect of SWOT. We find a globally consistent negative difference (SWOT minus ICESat‐2) of −0.25 m over the 1‐year period. This difference is dependent on season, amplifying by more than double from −0.15 m (warm) to −0.34 m (cold), with peak monthly differences nearly reaching −1 m. This study provides a framework for reconciling SWOT and ICESat‐2 observations, enabling long‐term, high‐resolution records of glacial lake variability.