Microalgal bacterial floc (MaB-floc) reactors have been suggested as a more sustainable secondary waste-water treatment. We investigated whether MaB-flocs could be used as tertiary treatment. Tertiary influent has a high inorganic/organic carbon ratio, depending on the efficiency of the secondary treatment. In this study, the effect of this inorganic/organic carbon ratio on the MaB-flocs performance was determined, using three sequencing batch photo-bioreactors. The MaB-flocs were fed with synthetic wastewater containing 84, 42, and 0 mg L-1 C-KHCO3 supplemented with 0, 42, 84 mg L-1 C-sucrose, respectively, representing inorganic versus organic carbon. Bicarbonate significantly decreased the autotrophic index of the MaB-flocs and resulted in poorly settling flocs. Moreover, sole bicarbonate addition led to a high pH of 9.5 and significant lower nitrogen removal efficiencies. Sucrose without bicarbonate resulted in good settling MaB-flocs, high nitrogen removal efficiencies and neutral pH levels. Despite the lower chlorophyll a content of the biomass and the lower in situ oxygen concentration, 92-96% of the soluble COD-sucrose was removed. This study shows that the inorganic/organic carbon ratio of the wastewater is of major importance and that organic carbon is requisite to guarantee a good performance of the MaB-flocs for wastewater treatment. Biotechnol. Bioeng. 2011;108: 549-558. (C) 2010 Wiley Periodicals, Inc.