BACKGROUND: Simultaneous nitrification-denitrification (SND) in biological wastewater treatment occurs under aerobic conditions in flocs and granules, exhibiting aerobic and internal anoxic zones; SND depends on dissolved oxygen concentration. Aerobic denitrification (AD) is an advantageous process because control of aeration is not required. In the present study, the effects of anoxic/aerobic conditions and size of microbial aggregates on the AD process were evaluated using sequencing batch reactors (SBR) with activated sludge (anoxic/aerobic SBR AS ) or aerobic granules (SBR AG ).RESULTS: Nitrogen mass balances were used to estimate nitrogen assimilation, nitrification and denitrification. An oxygen diffusion model was proposed to evaluate oxygen profiles in the microbial aggregates determining the contribution of AD on nitrogen removal. At COD:N ratio = 100:10, fully aerobic biomass was predicted for all flocs in SBR AS and for 82% of the granules in SBR AG . In SBR AS , intracellular carbon storage was favored in the anoxic phase; nitrification was followed by AD, achieving 67% inorganic nitrogen (Ni) removal. In SBR AG , SND was 55% and Ni removal 51%. For SBR AG , genomic analysis described microbial community and nitrogen metabolic pathways were proposed. Heterotrophic nitrification-aerobic denitrification (HNAD) was proposed as the main nitrogen removal process. At COD:N = 100:15, 80% of the granules developed internal anoxic zones; anoxic denitrification predominated, allowing treatment of a higher nitrogen load with similar Ni removal. CONCLUSIONS: Biological processes without oxygen control are simpler to operate. For anoxic/aerobic SBR, high Ni removal efficiency was achieved even with 3.5-5.4 mg O 2 L −1 at the center of the flocs, as predicted by the diffusion model. In aerobic granular systems, SND carried out by HNAD bacteria constitutes a promising approach for nitrogen removal.