Addition of oxygen to surface-flow wetland mesocosms treating synthetic secondary effluent resulted in a significant increase in ammonia oxidation potential in sediment compared to non-oxygenated controls. Ammonia oxidation potential in oxygenated wetland sediment (1.2–3.5 mg N g dw-1 d-1) was 2–3 orders of magnitude higher than those measured in sediment and soil systems reported in the literature. Phylogenic analysis of sediment from the two treatments revealed substantial differences in microbial diversity including the presence of ammonia-oxidizing bacteria (Nitrosomonas oligotropha) and denitrifying bacteria only in oxygenated sediment, and an increase in the diversity of aerobic phototrophs and methanotrophs in control sediment. These observations supported the contention by Palmer et al. (2009) that oxygenation ‘activated’ nitrifying bacteria in wetland sediment leading to high rates of biological ammonia oxidation.