The capacity of aqueous fluids to mobilize rare Earth elements is closely related to their molecular structure. In this study, first-principle molecular dynamics simulations are used to investigate the complex formation of yttrium with chloride and fluoride under subduction-zone conditions. The simulations predict that yttrium–fluoride complexes are more stable than their yttrium–chloride counterparts but likely less abundant due to the very low fluoride ion concentration in natural systems.