Purpose Nitrogen (N) application in excess of assimilatory capacity for aquaculture ponds can lead to water-quality deterioration through ammonia accumulation with toxicity to fish. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) potentially process extra ammonium, so their abundance and diversity are of great ecological significance. This study aimed to reveal variations in communities of AOA and AOB as affected by aquaculture activities. Materials and methods From June to September 2012, water and sediments were sampled monthly in three ponds feeding Mandarin fish in a suburb of Wuhan City, China. Molecular methods based on ammonia monooxygenase (amoA) gene were used to determine abundance and diversity of AOA and AOB in the sediments. Results and discussion The pond with the highest fish stock had the highest nutrient loadings in terms of different forms of N and carbon (C) in both sediment and water. The abundance and diversity of AOB were significantly higher than those of AOA in the sediment. The AOB abundance showed a significantly positive relationship to concentration of soluble reactive phosphorus (SRP) in interstitial water, and both abundance and diversity of AOA were significantly negative to concentration of ammonium in interstitial water. Furthermore, AOA species affiliated to Nitrososphaera-like and Nitrosophaera Cluster was distinguishable from those observed in other aquaculture environments. Conclusions Nutrients in sediment were enriched by intensive aquaculture activity, among which organic N and C, together with ammonium and SRP, shaped the communities of ammonia oxidizers, with AOB dominating over AOA in terms of abundance and diversity.