Fouling of the anion exchangers with organic compounds is a very common phenomenon. These compounds adsorb on the anion exchangers surfaces causing a decrease in the ion-exchange capacity. In practice, the performance of ion exchanger is generally assessed based on the breakthrough curves and the studies of the adsorption kinetics. There is little research in the literature concerning the surface changes of the resin beads. The image analysis enables recognition of the beads morphology, and Fourier-transform infrared (FTIR) spectroscopy enables detection of the foulants. To the authors’ knowledge, the application of these methods is a new approach to the organic fouling phenomenon. In this paper, image and FTIR analyses as well as scanning electron microscopy (SEM) were applied to assess the ageing process of two strongly basic anion exchangers in the process of treating of effluent containing high concentration of nitrites and nitrates. Effluent from sludge derived from fermentation chambers, dewatered on filter presses, and subsequently subjected to biological and membrane processes was fed through anion exchangers. The image, SEM and FTIR analyses indicated the accumulation of humic acids, which remained on the beads surface after regeneration, causing changes in the beads shape from circular to more elongated.