In this study, the lab-scale SBRs envisaged as external growth reactors for bio-flocs technology aquaculture ponds were able to provide adequate ammonia removal. Significant nitrogen assimilation was exhibited by the heterotrophic microbial biomass present using both glycerol and acetate as carbon source. This could be accomplished without leaving excessive amounts of carbon in the effluent, provided that an optimal C/N ratio ranging between 10 and 15 was maintained. Moreover, the quality of the bio-flocs in terms of protein content was similar to fish feed while the accumulation of PHB can represent a major added value.