Magnetic (Fe3O4) and nonmagnetic (SiO2 and TiO2) nanoparticles were decorated on their surface with N-[(3-trimethoxysilyl)propyl]ethylenediamine triacetic acid (TMS-EDTA). The aim was to investigate the influence of the substrate on the behavior of these immobilized metal coordinating groups. The nanoparticles functionalized with TMS-EDTA were used for the adsorption and separation of trivalent rare-earth ions from aqueous solutions. The general adsorption capacity of the nanoparticles was very high (100 to 400 mg/g) due to their large surface area. The heavy rare-earth ions are known to have a higher affinity for the coordinating groups than the light rare-earth ions but an additional difference in selectivity was observed between the different nanoparticles. The separation of pairs of rare-earth ions was found to be dependent on the substrate, namely the density of EDTA groups on the surface. The observation that sterical hindrance (or crowding) of immobilized ligands influences the selectivity could provide a new tool for the fine-tuning of the coordination ability of traditional chelating ligands.