Accurate estimates of microbial population concentrations and the direct, in situ determination of kinetic parameters could improve the calibration and validation of existing mechanistic mathematical models of biological nutrient removal activated sludge systems. Oligonucleotide probe hybridizations show promise for measuring concentrations and in situ specific growth rates of microbial populations. The most common targets for oligonucleotide probes are the phylogenetically conserved ribosomal RNA molecules. Recent advances in hybridization techniques have improved the quantitative nature of ribosomal RNA based assays. However, correlations between concentrations of 'theoretical' microbial populations predicted by mechanistic models and quantitative information obtained with oligonucleotide probe hybridizations are not yet developed. Future work should develop such correlations, while addressing the limitations of the molecular assays.