A polymeric ion-exchange resin, incorporating methyl-amino-phosphonic (TP260) functionalities, and a solvent impregnated resin (SIR) incorporating tri-methylpentylphosphinic acid (TP272), were evaluated for the selective separation of Rare Earth Elements (REE) from Transition (TE), post -Transition (PTE), and Alkaline Earth (AE) Elements in acidic mine waters (AMW). The influence of the functional groups nature and the acidity dependence were studied and their effects on efficiencies for REE removal and separation from TE/PTE were analysed Both resins provided good separation factors of REE from TE/PTE by acidity control of the treated effluent once Fe(III), the major component in AMW, had been removed by precipitation. The TP272 resin, containing tri-methylpentylphosphinic acid (Cyanex 272) onto the polymeric network, showed higher affinity towards Heavy REE (HRRE) than for Light REE (LRRE) by acidity control (pH > 4). Higher pre-concentration factors were achieved for TP272 impregnated resin (e.g., 20–30) in comparison with the TP260 phosphonic resin (2−5), as the pH extraction window is in the moderate pH region (1−5). The integration in series of both resins could be used to separate and recover HREE and LREE from TE/PTE from AMW generated concentrates could be used to recover REE as secondary resources for the clean energy technology industry.