The ion exchange of ammonia in a synthetic zeolite has been investigated in the presence of Biofilm of nitrifying bacteria. The Biofilm has been cultivated on the zeolite carrier under different hydrodynamic conditions in a plug flow reactor and in a fluidized bed reactor. Samples of the carrier covered by Biofilm have been withdrawn from the reactors and packed into a miniature ion exchange column that has been used to analyze the ion exchange characteristics, i.e., to determine ion exchange equilibria and the mass transport kinetics. For this purpose, the breakthrough curves have been registered at different ammonia loadings and different concentrations of sodium bicarbonate in the solution. To analyze the mass transport mechanism and quantify kinetic coefficients, we have exploited a linear driving force model (i.e., the LDF model) and the generalized model. The ion exchange and mass transfer characteristics of the Biofilm-covered carrier have been compared to those of the virgin zeolite. The effect of Biofilm on the mass transfer kinetics and ion exchange capacity was found to be induced by swelling properties of zeolite.