Ion-exchange (IX) resins incorporating single functional groups (sulfonic or amino-phosphonic) and two functional groups (sulfonic and phosphonic) were evaluated for selective recovery of Rare Earth Elements (REEs) from acidic mine waters (AMW). The composition of AMW solution, complexing properties of the functional group, and acidity were investigated as key parameters for concentration and separation of REEs from transition elements (TEs). Fe has to be removed from AMW to enable REE recovery and here the AMW was treated with NaOH solutions to reach pH 3.9 where Fe(III) was selectively removed (≤99%) by precipitation of schwertmannite. Single functional IX resin containing a sulfonic group displayed a higher REE recovery efficiency and separation ratio than observed for the bi-functional resin (sulfonic/phosphonic). Concentration factors for REEs between 30 and 40 were achieved using regeneration cycles with H2SO4. The performance of the aminophosphonic resin showed lower separation factors for REEs from TEs than the two resins containing sulfonic groups. IX resins performance was improved by tuning the acidity to match the functional group reactivity, where pH adjustment to the range of 0.5–2.0 provided the highest REE/TE separation factor for the single sulfonic resin followed by the bifunctional resin. The integration of an elution cycle using Na2-EDTA/NH4Cl mixtures strongly increases the concentration factors of REE and Light REE (LREE) concentration factors of up to 260 were achieved for the single functional sulfonic resin.