Geological 3D modeling delivers essential information on the distribution of enrichment zones and structures in (complex) mineral deposits and fosters a better guidance to subsequent exploration stages. The Paleoproterozoic Epembe carbonatite complex showcases the close relation between enrichment of specific elements (Nb, Ta, P, Total Rare Earth Element (TREE) + Y) and shear zones by structural modeling combined with geochemical interpolation. Three-dimensional fault surfaces based on structural field observations, geological maps, cross-sections, and drillhole data are visualized. The model shows a complex, dextral transpressive fault system. Three-dimensional interpolation of geochemical data demonstrates enrichment of Nb, Ta, P, and TREE + Y in small, isolated, lens-shaped, high-grade zones in close spatial distance to faults. Based on various indicators (e.g., oscillating variograms, monazite rims around the apatite) and field evidence, we see evidence for enrichment during hydrothermal (re-)mobilization rather than due to magmatic differentiation related to the formation of the alkaline system. This is further supported by geostatistical analysis of the three-dimensional distribution of Nb, Ta, P, and Light Rare Earth Elements (LREE) with respect to discrete shear zones.