Single photon sensitive airborne Light Detection And Ranging (LiDAR) enables a higher area performance at the price of an increased outlier rate and a lower ranging accuracy compared to conventional Multi-Photon LiDAR. Single Photon LiDAR, in particular, uses green laser light potentially capable of penetrating clear shallow water. The technology is designed for large-area topographic mapping, which also includes the water surface. While the penetration capabilities of green lasers generally lead to underestimation of the water level heights, we specifically focus on the questions of whether Single Photon LiDAR (i) is less affected in this respect due to the high receiver sensitivity, and (ii) consequently delivers sufficient water surface echoes for precise high-resolution water surface reconstruction. After a review of the underlying sensor technology and the interaction of green laser light with water, we address the topic by comparing the surface responses of actual Single Photon LiDAR and Multi-Photon Topo-Bathymetric LiDAR datasets for selected horizontal water surfaces. The anticipated superiority of Single Photon LiDAR could not be verified in this study. While the mean deviations from a reference water level are less than 5 cm for surface models with a cell size of 10 m, systematic water level underestimation of 5–20 cm was observed for high-resolution Single Photon LiDAR based water surface models with cell sizes of 1–5 m. Theoretical photon counts obtained from simulations based on the laser-radar equation support the experimental data evaluation results and furthermore confirm the feasibility of Single Photon LiDAR based high-resolution water surface mapping when adopting specifically tailored flight mission parameters.