Due to the regulations on drinking water quality becoming stricter, it is important to remove natural organic matter (NOM) from water. The ion exchange process that uses synthetic resins is among the many processes that allow it. The suitability of two macroporous polystyrene resins: A100 and BD400FD for the removal of NOM from water and also the integrated process combining ion exchange with ultrafiltration were evaluated. The impact of process set-up and selected water parameters on the treatment effectiveness was compared. XAD resin fractionation was used to characterize removed NOM. The results showed that tested resins can be effectively used to remove NOM from water. Performing the ion exchange in a flow set-up resulted in better purification effects when compared to a batch set-up. The A100 resin was more effective. An increase in pH resulted in a slight decrease in NOM removal efficiency, while an increase in temperature increased it. The use of the integrated process resulted in significant improvements in water quality due to the combined effect. Fractional analysis showed a change in the treated water composition when compared to raw samples. Preferential removal of higher molecular weight hydrophobic fractions and also poor hydrophilic fractions elimination were observed.