The objective of this study was to analyze the efficiency of water treatment in the ion exchange process (with the use of MIEX® resin), in ultrafiltration, and in a hybrid process composed of ion exchange and ultrafiltration. The influence of MIEX® resin dose on the efficiency of natural organic matter (NOM) removal was analyzed. CeramINSIDE ceramic membrane modules (TAMI Industries) were used in the experiments. Based on obtained results, it might be stated that magnetic ion-exchange resin is effective in NOM separation from natural waters. The use of the MIEX®DOC process prior to ultrafiltration increased permeate quality and partly reduced the intensity of membrane fouling, especially for high MWCO membranes. Even very low MIEX® resin doses improved final water quality. Moreover, water treatment in the hybrid process eliminated secondary pollution of water by residual resin.