The Pacific oyster (Magallana gigas) is an invasive species in the Wadden Sea transforming parts of it permanently. M. gigas, as an ecosystem engineer, builds reef structures that are characterized by highly complex and variable surfaces consisting of densely packed, sharp-edged individuals connected with cement-like bonds. To investigate the interactions between reef structure, shape and formation and wave as well as tidal currents, an understanding of the surface roughness is essential. This work reports on observations of oyster reefs for which seven new structural classes (Central Reef, Transitional Zone, Cluster I, Cluster II, Patch I, Patch II, and Garland) are proposed. For each class, high resolution Digital Elevation Models (DEMs) have been elaborated based on Structure-from-Motion (SfM) photogrammetry and analyzed using spatial statistics. By determining probability density functions (PDFs), vertical porosity distributions, abundances, orientations and second-order structure functions (SSFs), topographical parameters that influence the hydraulic bed roughness have been determined. The results suggest, that by applying the structural classification and their distinct topographical roughness parameters, the oyster reef surfaces can be described appropriately accounting for their complexity. The roughness accounts to a total roughness height kt = 103 ± 15 mm and root-mean-square roughness height krms = 23 ± 5 mm. These values were found similar across all structural classes, yet the shape of the PDFs reveal differences. With decreasing abundance, the distributions become more positively skewed and are characterized by more extreme outliers. This is reflected in the higher statistical moments, as the skewness ranges between Sk = 0.4–2.1 and the kurtosis between Ku = 2.2–11.5. The analysis of the orientations and the SSFs confirms anisotropic behavior across all structural classes. Further, the SSFs reveal the oyster shells as significant roughness elements with exception of Cluster I and II, where the clusters are identified as significant roughness elements. The provided set of topographical roughness parameters enhances the knowledge of oyster reef surfaces and gives insights into the interactions between biogenic structure and surrounding hydrodynamics. The new intra-reef classification allows for more accurate determination of the overall roughness as well as the population dynamics of the habitat forming oyster. Combined with hydraulic measurements, the results can be used to estimate the hydraulic bed roughness induced by the oyster reef surfaces. Copyright © 2022 Hitzegrad, Brohmann, Pfennings, Hoffmann, Eilrich, Paul, Welzel, Schlurmann, Aberle, Wehrmann and Goseberg.