Model-based soil erosion studies have increased in number, given the availability of geodata and the recent technological advances. However, their accuracy remains rather questionable since the scarcity of field records hinders the validation of simulated values. In this context, this study aims to present a method for measuring sediment deposition at a typical Mediterranean catchment (870 ha) in Greece through high spatial resolution field measurements acquired by an Unmanned Aerial Vehicle (UAV) survey. Three-dimensional modeling is considered to be an emerging technique for surface change detection. The UAV-derived point cloud comparison, applying the Structure-from-Motion (SfM) technique at the Platana sediment retention dam test site, quantified annual topsoil change in cm-scale accuracy (0.02–0.03 m), delivering mean sediment yield of 1620 m3 ± 180 m3 or 6.05 t ha−1yr−1 and 3500 m3 ± 194 m3 or 13 t ha−1yr−1 for the 2020–2021 and 2021–2022 estimation. Moreover, the widely applied PESERA and RUSLE models estimated the 2020–2021 mean sediment yield at 1.12 t ha-1yr−1 and 3.51 t ha-1yr−1, respectively, while an increase was evident during the 2021–2022 simulation (2.49 t ha−1yr−1 and 3.56 t ha−1yr−1, respectively). Both applications appear to underestimate the net soil loss rate, with RUSLE being closer to the measured results. The difference is mostly attributed to the model’s limitation to simulate gully erosion or to a C-factor misinterpretation. To the authors’ better knowledge, this study is among the few UAV applications employed to acquire high-accuracy soil loss measurements. The results proved extremely useful in our attempt to measure sediment yield at the cm scale through UAV-SfM and decipher the regional soil erosion and sediment transport pattern, also offering a direct assessment of the retention dams’ life expectancy.