Coagulation/flocculation (C/F)/dissolved air flotation (DAF) and C/F/sedimentation (S) experiments were performed using natural waters to evaluate the influence of the water background organic matrix (type and concentration) on the Microcystis aeruginosa removal by both processes. Two natural waters collected at Alcantarilha Water Treatment Plant (Algarve, Portugal), raw water (RW) and ozonated water (OW), spiked with cultured cells of M. aeruginosa were used since they represent two types of natural organic matter (NOM)-preozonation is the process that mostly affects NOM molecular weight and hydrophilicity. Results obtained, compared to those earlier found with tap water (TW), showed that NOM had a negative influence on the cyanobacterial cells removal, both in terms of removal efficiencies and coagulant demand, for higher coagulant doses were needed to destabilise the particles present in the water. OW showed higher removals than RW, especially for C/F/S. These results were attributed to the preozonation enhancing effect on C/F, since it causes NOM oxidation and particle destabilisation, responsible for increased organics and particle removal. C/F/DAF was less influenced by the NOM content (RW and OW versus TW) and type (RW versus OW) than C/F/S which required heavier flocs for effective separation. In addition, C/F/DAF process showed the best cyanobacterial removal efficiencies, higher than 92%, as well as the lowest residuals for lower optimal coagulant dose. Extracellular microcystins were practically not removed from the water by both processes, but no release of toxins was found. (c) 2006 Elsevier B.V. All rights reserved.