Eu(III)–humic acid (HA) aggregates are investigated in situ by laser scanning luminescence microscopy (LSLM) and scanning transmission X-ray microscopy (STXM). C 1s-NEXAFS spectromicroscopy reveals optically dense zones rich in carboxyl groups surrounded by less absorbing material. The Eu(III) distribution within these zones is mapped by LSLM using laser excitation. In the LSLM micrographs confined patches with increased Eu(III) luminescence are shown to be embedded in a matrix of lower luminescence. The agreement of the morphologies revealed by both methods confirms the Eu(III) induced HA-segregation into fractions of varying chemical functionality.