AbstractSoil surface roughness (SSR) is an important factor in controlling sediment and runoff generation, influencing directly a wide spectrum of erosion parameters. SSR is highly variable in time and space under natural conditions, and characterizing SSR to improve the parameterization of hydrological and erosion models has proved challenging. Our study uses recent technological and algorithmic developments in capturing and processing close aerial sensing data to evaluate how high‐resolution imagery can assist the temporally and spatially explicit monitoring of SSR. We evaluated the evolution of SSR under natural rainfall and growing vegetation conditions on two arable fields in Denmark. Unmanned aerial vehicle (UAV) photogrammetry was used to monitor small field plots over 7 months after seeding of winter wheat following conventional and reduced tillage treatments. Field campaigns were conducted at least once a month from October until April, resulting in nine time steps of data acquisition. Structure from motion photogrammetry was used to derive high‐resolution point clouds with an average ground sampling distance of 2.7 mm and a mean ground control point accuracy of 1.8 mm. A comprehensive workflow was developed to process the point clouds, including the detection of vegetation and the removal of vegetation‐induced point cloud noise. Rasterized and filtered point clouds were then used to determine SSR geostatistically as the standard deviation of height, applying different kernel sizes and using semivariograms. The results showed an influence of kernel size on roughness, with a value range of 0.2–1 cm of average height deviation during the monitoring period. Semivariograms showed a measurable decrease in sill variance and an increase in range over time. This research demonstrated multiple challenges to measuring SSR with UAV under natural conditions with increasing vegetation cover. The proposed workflow represents a step forward in tackling those challenges and provides a knowledge base for future research. © 2020 John Wiley & Sons, Ltd.