Ice cliffs within a glacier represent a challenge for the continuity equations used in many glacier models by interrupting the validity of input parameters. In the case of Gourdon Glacier on James Ross Island, Antarctica, a ∼300–500 $\mathrm{m}$ high, almost vertical cliff, separates the outlet glacier from its main accumulation area on the plateau of the island. In 2017 and 2018 we conducted ice thickness measurements during two airborne ground penetrating radar campaigns in order to evaluate differences to older measurements from the 1990s. The observed differences are mostly smaller than the estimated error bars. In comparison to the in situ data, the published “consensus ice thickness estimate” strongly overestimates the ice thickness at the outlet. We analyse three different interpolation and ice thickness reconstruction methods. One approach additionally includes the mass input from the plateau. Differences between the interpolation methods have a minor impact on the ice discharge estimation if the used flux gates are in areas with a good coverage of in situ measurements. A much stronger influence was observed by uncertainties in the glacier velocities derived from remote sensing, especially in the direction of the velocity vector in proximity to the ice cliff. We conclude that the amount of in situ measurements should be increased for specific glacier types in order to detect biases in modeled ice thickness and ice discharge estimations.