The aerobic digestion of two different waste activated sludges was examined using a semi-continuous flow scheme and variable raw sludge loading rates. Due to daily perturbations of the system, resulting from sludge withdrawal/addition, the analysis of kinetic decay rates required a modification of the classic methodology, which could account for these external sources of variability in process performance analysis. The resultant kinetic decay coefficients reflected this operational variability, due both to observable and unobservable sources; at the same time, these values were able to describe the dynamic biological processes of the aerobic digester, and reflect the trends seen in volatile mass reduction. It was proposed that these values could subsequently be used in a valid analysis of temperature sensitivity within the digester, such that temperature ranges to be targeted for economical digester performance enhancement could be easily selected.