A simplified model of microbial aggregates is developed to evaluate how the key features of aggregation affect the stability of nitrification in multiple-species biofilms and flocs. The foundation of the model is a layered system in which each layer contains a different type of biomass, includes mass-transport resistance for all substrates (i.e., COD, NH4+, and O2), and included formation and consumption of soluble microbial products. The model describes how the outer biofilm layer of heterotrophs protects the inner layers of nitrifiers and inert biomass from detachment, so that an inner layer can have a low specific detachment-loss rate. This protecting function is not important for suspended flocs, because the entire floc is wasted. Comparison of biofilm and suspended flocs shows that the protecting function of the biofilms provides greater nitrification stability. The model also demonstrates that extensive heterotrophic growth induced by high organic loading can cause a deterioration of nitrification when the dissolved oxygen is depleted in the inner layer of the aggregate. Although it is based on a simplified spatial distribution, the aggregate model identifies key differences among biofilm, floc, and dispersed-growth processes.