Models for engineering design of nitrifying systems use one ammonia oxidizer biomass (AOB) state variable. A simple extension using two AOB populations allows a more accurate prediction of nitrification systems at switching process environments. These two AOB subpopulations are characterized by two different sets of kinetic parameters. Selection pressure and competition between the two functional AOB populations are determined by process conditions as demonstrated by three case studies: Case study I describes dynamics of two AOB populations showing different temperature sensitivities (modified Arrhenius term on growth and decay) when bioaugmented from the warm sidestream treatment environment to the cold mainstream and vice-versa. Case study II investigates competition between fast growing μ-strategists and k-strategists adjusted to low ammonia levels depending on the internal mixed liquor recycle rate (IMLR). Case study III shows that AOB transferred from the waste activated sludge of an SBR to the parallel continuous flow system with different decay kinetics can overgrow or coexist with the original population.