Many dairy industries have been using SBR wastewater treatment plants because they allow optimal working condition to be reached. However, to take advantage of SBR capabilities, strong process automation is needed. The aim of this work is to study the factors that influence SBR performance to improve modelling and control. To better understand the whole process we studied the kinetic modelling, the carbon removal mechanism and the relation between reactor performance, aerobic heterotrophic activity and bacterial population dynamics (by terminal restriction fragment length polymorphisms of 16S rDNA, T-RFLP). The heterotrophic activity values presented high variability during some periods; however, this was not reflected on the reactor performance. As sludge health indicator, the average activity in a period was better than individual values. Although all the carbon removal mechanisms are still unclear for this process, they seemed to be influenced by non-respirometric ways (storage, biosorption, accumulation, etc.). The variability of heterotrophic activity could be correlated with the bacterial population diversity over time. Despite the high variability of the activity, a simple kinetic model (pseudo ASM1) based on apparent constant parameters was developed and calibrated. Such modellisation provided a good tool for control purposes.