Describing the structural complexity of seabeds is of primary importance for a number of geomorphological, hydrodynamical and ecological issues. Aiming to bring a decisive insight on the long-term development of a unified view, the present study reports on a comparative multi-site analysis of high resolution topography surveys in rough nearshore environments. The nine study sites have been selected to cover a wide variety of topographical features, including rocky and coral seabeds. The topography data has been processed to separate roughness and bathymetry-related terrain features, allowing to perform a comprehensive spectral and statistical analysis of each site. A series of roughness metrics have been tested to identify the most relevant estimators of the bottom roughness at each site. The spectral analysis highlights the systematic presence of a self-affine range of variable extension and spectral slope. The standard deviation of the seabed elevation varies from 0.04 to 0.77 m. The statistical and multi-scale analysis performed on the whole set of roughness metrics allows to identify connection between metrics and therefore to propose a reduced set of relevant roughness estimators. A more general emphasis is placed on the need to properly define a unified framework when reconstructing roughness statistics and bathymetry from fine seabed topographical data.