The objective of this work was to compare the affinity of well characterized NOM fractions isolated from two surface waters with strong (gel matrix and macroporous matrix) and weak anion exchange resins (AER) using batch experiment conditions. The structural characterization of the fraction of NOM has shown that the higher the hydrophilic character, the lower the C/O atomic ratio, the lower the SUVA, the lower the aromatic carbon content and the lower the molecular weight. In general (not always), strong AER was more efficient to remove DOC than weak AER. For the same water source (Suwannee River), the higher the molecular weight of the NOM fraction, the lower the affinity with AER. Increasing the ionic strength favored the removal of the hydrophobic NOM fraction (“salting out” effect) while increasing the pH apparently reduced the removal of the hydrophilic NOM fraction. Results were discussed in terms of size exclusion, adsorption, anion exchange and also hydrophobic/hydrophilic repulsion.