The determination of different rates of endogenous nitrate respiration due to biomass stratification throughout the depth of a sludge blanket is essential to assess the factors affecting the sludge rising in secondary clarifiers. In this study, an extension of the solids flux theory in conjunction with nitrate mass balance was used to model the fate of nitrate in a sludge settling column. The model-predicted nitrate concentrations agree well with those experimentally determined. A new term, sludge stability index, was introduced to reflect the sludge rising time and the corresponding critical nitrate concentration necessary for causing sludge rising. The model predicted well the observed sludge rising times occurring under batch settling column experiments with initial biomass and nitrate concentration ranging from 2000 to 5000 mg l −1 and 10 to 30 mg-N l −1, respectively. Furthermore, simulation results indicated that both the sludge rising time and CNC are significantly affected by k ENR.