Iron oxide encrustations are formed on black slate surfaces during oxidative weathering of iron sulfide and phosphate bearing, organic matter-rich slates. Synchronously, trace elements are released during ongoing weathering. Laser ablation ICP-MS analyses of a weathered and encrusted slate showed that major portions of the V, Cu, As, Mo, Pb, Th, and U reside in the encrustation.Recently a potential relationship between several micrometer to 500 nm surface topography roughness of such encrustations and its uranium concentration was shown. Based on laser scanning microscopy measurements, the present study shows that this interrelation must be expanded to small submicron-sized half-pores with diameters between 100 nm and 500 nm. We demonstrate that the relationship is not limited to topography variations of a single encrustation in the hand-specimen scale. Surface topography and geochemical analyses of iron oxide encrustations from several locations but from the same geochemical environment and with similar weathering history showed that the concentrations of U, P, Cu, and Zn correlate inversely with the surface roughness parameter F. This parameter represents the total surface area and is - in this case - a proxy for the root-mean square surface roughness Rq.This study substantiates the environmental importance that micrometer- to submicrometer topography variations of fluid-rock interfaces govern the trapping of trace elements.