Purpose <p>Ammonia and sulfur compounds in sediments constitute two major threats to freshwater aquaculture pond and surrounding environments. This study aims to explore the effects of sulfate elevation on ammonia oxidization in aquaculture pond sediment.</p> Methods <p>In this study, mesocosm systems were established using sediment and water collected from a freshwater aquaculture pond, and treated with Na₂SO₄ of final concentrations of about 0 (control), 30 (T1 group), 150 (T2 group), and 500&#xa0;mg L⁻¹ (T3 group). The effects of SO₄²⁻ as well as its reduced sulfides on ammonia-oxidizing microorganisms, including bacteria (AOB) and archaea (AOA), and anaerobic ammonium oxidation (anammox) bacteria in surface sediments were analyzed.</p> Results <p>The potential nitrification rates and anammox rates were decreased, but the copy numbers of AOA, AOB, and anammox bacteria in the T2 and T3 groups were slightly increased compared to the control group. Clear differences of AOA and AOB compositions were found between the T2/T3 group and control group, while the differences of anammox bacterial communities between these groups were relatively small. The co-occurrence correlations among different ammonia-oxidizing microbial taxa were greatly reduced by treatment of high concentrations of sulfate. Compared with AOA and AOB, anammox bacterial communities were less influenced by sediment environmental change induced by sulfate addition, and were positively correlated with nitrite and ammonia concentrations.</p> Conclusion <p>Our results demonstrated that anammox bacteria could be more resilient than AOA and AOB communities, and thus would be important in ammonia transformation in sulfur-rich freshwater aquaculture pond sediments.</p>