Yttrium belongs to the rare earth elements (REEs) together with lanthanides and scandium. REEs are commonly used in modern technologies, and their limited supply has made it necessary to look for new alternative resources. Acid mine drainage (AMD) is a potential resource since it is moderately enriched in REEs. In fact, in passive remediation systems, which are implemented to minimize the environmental impacts of AMD, REEs are mainly retained in basaluminite, an aluminum hydroxysulfate precipitate. In this study, the solid and liquid speciation and the local structure of yttrium are studied in high-sulfate aqueous solutions, basaluminite standards, and samples from remediation columns using synchrotron-based techniques and molecular modeling. Pair distribution function (PDF) analyses and ab initio molecular dynamics density functional theory models of the yttrium sulfate solution show that the YSO4+ ion pair forms a monodentate inner-sphere complex. Extended X-ray absorption fine structure (EXAFS) and PDF analyses show that Y is retained by basaluminite, forming a monodentate inner-sphere surface complex on the aluminum hydroxide surface. EXAFS of the column samples shows that more than 72% of their signal is represented by the signal of basaluminite with which YSO4+ forms an inner-sphere complex. The atomic view of the REE configuration in AMD environments could facilitate a deeper research of REE recovery from waste generated in AMD remediation systems.