Neodymium is a critical metal essential for advancing sustainable clean energy technologies, as it is a crucial component in the manufacturing of NdFeB permanent magnets, part of wind turbines, electric vehicles, and advanced electronics. Its recovery from secondary sources using electrochemical deposition in ionic liquids has the potential to sustainably achieve a closed-loop alternative to obtain the metal. The presence of water in low, specific concentrations in ionic liquid has been previously shown to catalyze electrodeposition of Nd with amplified current densities and easier reduction of Nd3+, but the structure(s) of the metal/mixed-ligand species that led to this amplification was previously only hypothesized. Stringently benchmarked quantum chemical calculations reveal a complex potential energy landscape that underpins the structural transformations arising from the introduction of water into the coordination sphere of Nd3+ surrounded by bis(trifluoromethanesulfonyl)imide (TFSI) anions. Three distinct changes were observed in the Nd3+-TFSI– complexes upon addition of water: (i) cis/trans transformation of TFSI, (ii) transition from bidentate to monodentate TFSI– coordination, and (iii) displacement of TFSI– ligands by water. Energetic analyses of these structural changes can explain experimentally observed water-loading effects regarding the ease of electrochemical reduction of Nd3+ and its deposition. These outcomes provide a platform for tuning ionic liquid media compositions to enhance rare-earth metal recovery.