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Iodinated contrast media (ICM) are persistent and ubiquitous water pollutants. Because of their high water solubility and biochemical stability, their phase-separation and recovery from the aquatic environment is very difficult. Here, borate was chosen as a complexing agent of the two diagnostic aids iomeprol and iopamidol in order to provide them with a negative charge and to fix the resulting adducts on Dowex 1X4 ion exchangers. A systematic characterization study of the complex by means of capillary zone electrophoresis and 11B NMR revealed that iomeprol and iopamidol interact with borate anions in aqueous solutions giving a 1:1 single-charged adduct and that the association constant at 25 °C for both contrast agents is highest at pH 10.5. These findings allowed the proper calibration of experimental parameters for further batch adsorption–desorption trials, where the two ICM were shown to be almost completely removed from the water phase and released from the solid sorbents in mild conditions, enabling the recovery of functional resin.