Inhibition of nitrification in the presence of low oxygen concentrations (below 1.2 mg/L) and temperature dependency at oxygen saturation levels were observed in an aerated treatment pond system with biofilm promoting mats in two parallel ponds for remediation of ammonium, methyl tertiary butyl ether (MTBE), and benzene-contaminated groundwater. Within the first 18 months, at an average oxygen concentration of 0.7 ± 0.5 mg/L along the ponds, no significant decrease of ammonium or significant formation of nitrification products were observed. After increasing the aeration to oxygen saturation levels, the ammonium removal increased up to a maximum of 27%, with concomitant formation of nitrite and nitrate (up to 26 and 0.6 mM). The subsequent reduction of aeration in one pond to the previous level resulted in a definitive stop of nitrification, while, in the other pond, nitrification was well-correlated with the water temperature, reaching up to 45% ammonium removal.