The natural organic matter (NOM) from a large quantity (1000 L) of groundwater from a Western Australian bore was isolated and separated into three polarity-based fractions (hydrophobic, transphilic and hydrophilic) using an XAD-8/XAD-4 resin fractionation method. These NOM fractions were separately treated by the magnetic ion exchange (MIEX®) resin process to investigate the effect of the MIEX® process on different organic polarity-based fractions. MIEX® was effective for targeting the more non-polar (hydrophobic) and the intermediate polarity (transphilic) NOM, with similar DOC removals observed for both the hydrophobic and transphilic fractions from this groundwater. Analysis of the NOM samples before and after MIEX® treatment by SEC-OCD showed that, for the hydrophobic fraction, organic matter over a wide range of apparent molecular weights, was removed, with particularly good removal of the high molecular weight material. Includes 18 references, table, figures.