Two five-litre activated sludge (AS) bioreactors were operated for several months to demonstrate potential mill applications of a four-assay set, which has been proposed as a tool for monitoring the health of the AS microbial population. The set consists of three specific oxygen uptake rate (SOUR) determinations at different substrate concentrations (SOURat, SOURnmax and SOURtox where at, nmax and tox are defined as aeration tank, near maximum, and toxic, respectively), and a specific adenosine triphosphate (SATP) assay. Two disturbances were applied at different times to an AS system treating kraft effluent. First, temperature was increased from 25 to 40 degreesC, and second, a black liquor spill was simulated. The data before, during, and after these disturbances were statistically analyzed. From this analysis, we concluded that the four-assay set could be used as a microbial health characterization (MHC) tool. It allows an operator to correlate microbial changes with operating data over a medium-term time scale. We compared the values obtained during periods of upset in the system treating the kraft effluent, to the baseline data set determined from stable operation periods. This demonstrated how the four-assay set could be used as a biological early warning (BEW) tool. It allows a treatment system operator to make appropriate adjustments immediately after detecting values that fall outside the baseline data range.