The oxidation of ammonium in the vadose zone of soil aquifer systems is discussed and examined by detailed analysis of the depth profiles of dissolved oxygen, nitrate and ammonium concentrations in the vadose zone of a soil-aquifer treatment (SAT) system of a municipal wastewater treatment system of the Tel Aviv metropolitan area. Nitrification kinetics and ammonium adsorption capacity studies show that neither the nitrification rate nor the ammonium adsorption capacity controls the capacity of the Shafdan SAT system for ammonium removal. Evaluation of the ammonium adsorption capacity of the soil reveals that under ideal conditions, a depth of less than 50 cm is sufficient to adsorb all the ammonium supplied in a flooding cycle. In-field studies show that all the ammonium is concentrated within the first 80 cm of the vadose zone. A depth profile of the Potential Nitrification (P.N), a measure of the local amount and activity of nitrifiers, is presented for the first time in the vadose zone of a SAT system showing that there are sufficient nitrifiers to oxidize all the ammonia that is supplied in a flooding cycle within less than 2 h, under optimal microbiological conditions based on the existing nitrifiers and their spatial distribution. The biodegradation rate in the field corresponds to first order ammonium conversion with a kinetic coefficient of 8.0 ± 0.2 d-1. Accordingly, the average measured rate was 8.6 ± 5.8 mg NH4+-N per kg per d for in-field tests, which can be compared to the average P.N, with a value of 34.5 ± 16.8 mg NH4+-N per kg per d. The results suggest that a SAT design, taking into account full ammonium removal capacity, is feasible and can rely on the evaluation of the ammonium adsorption capacity in the SAT soil, the ammonium input and the P.N of the equilibrated target soil under conditions simulating the operation of the infiltrating basins.