Structure-from-Motion (SfM) photogrammetry has become a popular solution for three-dimensional topographic data collection in geosciences and can be used for measuring submerged bed surfaces in shallow and clear water systems. However, the performance of through-water SfM photogrammetry has not been fully evaluated for gravel-bed surfaces, which limits its application to the morphodynamics of gravel-bed rivers in both field investigations and flume experiments. In order to evaluate the influence of bed texture, flow rate, ground control point (GCP) layout, and refraction correction (RC) on the measurement quality of through-water SfM photogrammetry, we conducted a series of experiments in a 70 m-long and 7 m-wide flume with a straight artificial channel. Bed surfaces with strongly contrasting textures in two 4 m-long reaches were measured under five constant flow regimes with three GCP layouts, including both dry and underwater GCPs. All the submerged surface models with/without RC were compared with the corresponding dry bed surfaces to quantify their elevation errors. The results illustrated that the poorly sorted gravel-bed led to the better performance of through-water SfM photogrammetry than the bed covered by fine sand. Fine sediment transport caused significant elevation errors, while the static sand dunes and grain clusters did not lead to noticeable errors in the corrected models with dry GCPs. The elevation errors of the submerged models linearly increased with water depth for all the tested conditions of bed textures, GCP layouts, and discharges in the uncorrected models, but the slopes of the increasing relations varied with texture. The use of underwater GCPs made significant improvements to the performance of direct through-water SfM photogrammetry, but counteracted with RC. The corrected models with dry GCPs outperformed the uncorrected ones with underwater GCPs, which could still be used to correct the underestimation in surface elevation caused by RC. Based on the new findings, recommendations for through-water SfM photogrammetry in measuring submerged gravel-bed surfaces were provided.