The Anammox process allows a sustainable treatment of wastewater with high nitrogen content. Partial oxidation of ammonium to nitrite is a previous and crucial step. Given the variability on wastewater composition, the operation of sequencing batch reactors (SBR) for partial nitritation (PN) is very challenging. This work assessed the combined influence of influent characteristics and process loading rate. Simulation results showed that wastewater composition - Total nitrogen as ammonia (TNH) and total inorganic carbon (TIC) - as well as nitrogen loading rate (NLR) govern the outcomes of the reactor. A suitable effluent can be produced when treating wastewater with different ammonia levels, as long as the TIC:TNH influent molar ratio is around 1:1 and extreme NLR are avoided. The influent pH has a key impact on nitrite conversion by governing the CO2-bicarbonate-carbonate equilibrium. Finally, results showed that oxidation of biodegradable organic matter produces CO2, which acidifies the media and limits process conversion. (C) 2012 Elsevier Ltd. All rights reserved.