The dynamic reactor behaviour of a nitrifying inverse turbulent bed reactor, operated at varying loading rate, was described with a one-dimensional two-step nitrification biofilm model. In contrast with conventional biofilm models, this model includes the competition between two genetically different populations of ammonia-oxidizing bacteria (AOB), besides nitrite-oxidizing bacteria (NOB). Previously gathered experimental evidence showed that different loading rates in the reactor resulted in a change in the composition of the AOB community, besides a different nitrifying performance. The dissolved oxygen concentration in the bulk liquid was put forward as the key variable governing the experimentally observed shift from Nitrosomonas europaea (AOB1) to Nitrosomonas sp. (AOB2), which was confirmed by the developed one-dimensional biofilm model. Both steady state and dynamic analysis showed that the influence of microbial growth and endogenous respiration parameters as well as external mass transfer limitation have a clear effect on the competition dynamics. Overall, it was shown that the biomass distribution profiles of the coexisting AOB reflected the ecological niches created by substrate gradients.