A dynamic model describing integrated nitrification and denitrification by Nitrosomonas europaea and Pseudomonas sp. co-immobilized in the separate layers of double-layer gel beads is presented. The model describes diffusion of components, substrate utilization, and growth, all occurring simultaneously in the beads. Both internal and external mass transfer resistance are accounted for. The model predicts biomass and solute bulk concentrations, substrate consumption rates, product formation rates, and biomass and solute concentration profiles within the beads as a function of time. Fluctuations in substrate load, dilution rates, or mass transfer parameters can be accommodated as well. Intrinsic kinetic parameters of the microorganisms, internal and external mass transfer coefficients, initial conditions, bead concentration, and particle diameters are the input parameters. The model was evaluated by comparing experimental and predicted bulk concentrations and macroscopic consumption (production) rates in air-lift loop reactors containing double-layer gel beads. The reactors were run under both steady and dynamic operating conditions. Nitrification rates were determined by daily analysis of influent and effluent ammonia and nitrite concentrations, and denitrification rates were calculated from molecular nitrogen production rates measured by head-space analysis. Model predictions agreed reasonably well with the experimental results. Fluctuations in dilution rates and influent substrate concentrations were adequately described. Although further validation is still required, the model presented here has shown to describe satisfactorily the proposed system.