This study investigated the efficiency of a strongly basic macroporous anion exchange resin for the co-removal of Microcystin-LR (MCLR) and natural organic matter (NOM) in waters affected by toxic algal blooms. Environmental factors influencing the uptake behavior included MCLR and resin concentrations, NOM and anionic species, specifically nitrate, sulphate and bicarbonate. A860 resin exhibited an excellent adsorption capacity of 3800 μg/g; more than 60% of the MCLR removal was achieved within 10 min with a resin dosage of 200 mg/L (∼1 mL/L). Further, kinetic studies revealed that the overall removal of MCLR is influenced by both external diffusion and intra-particle diffusion. Increasing NOM concentration resulted in a significant reduction of MCLR uptake, especially at lower resin dosages, where a competitive uptake between the charged NOM fractions and MCLR was observed due to limited active sites. In addition, MCLR uptake was significantly reduced in the presence of sulphate and nitrate in the water matrix. Moreover, performance of the resin proved to be stable from one regeneration cycle to another. Approximately 80% of MCLR and 50% of dissolved organic carbon (DOC) were recovered in the regenerated brine. Evidences of resin saturation and site reduction were also observed after 2000 bed volumes (BV) of operation. For all the investigated water matrices, a resin dosage of 1000 mg/L (∼4.5 mL/L) was sufficient to lower MCLR concentration from 100 μg/L to below the World Health Organization guideline of 1 μg/L, while simultaneously providing more than 80% NOM removal.