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Natural organic matter (NOM) is present in all surface and ground waters and originates from degradation and by-products of living organisms and plants. NOM can be separated by HPLC-Organic Carbon Detection into five fractions: biopolymers, humic substances, building blocks, low molecular weight acids and low molecular weight neutrals. Water quality is affected by the presence of NOM (fractions) and moreover it can cause several issues during water treatment processes. Therefore, its removal by a variety of technologies is widely studied. Anion exchange resins (AER) can effectively remove a major part of this NOM, but due to its complex nature, the process is still not completely understood and optimized. In this work, the removal of NOM by macroporous styrenic weak (WBA), strong (SBA) and combined weak/strong (W/SBA) base anion exchange resins is studied. The resins were used in two industrial relevant counter ion forms: the OH- or free base form for SBA and WBA resins respectively, using an NaOH conditioning solution as applied in water demineralisation units and a Cl- form using NaCl for SBA resins and HCl for the WBA and W/SBA resins, as seen in drinking water treatment and Dupont’s recently developed weak basic NOM scavenger resins respectively. The effect of this conditioning on the equilibrium pH and driving forces for NOM removal in batch mode experiments using synthetic water containing model compounds for the different NOM fractions was investigated. This study demonstrated that next to AER resin selection, the conditioning procedure is an important parameter to be considered in the design of NOM removal processes, especially when specific NOM fractions are targeted.