Ammonia oxidation, driven by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), plays an important role in the global nitrogen cycle. However, the population and distribution of ammonia-oxidizing microorganisms in the sediments of urban rivers with intensive anthropogenic nitrogen inputs is still unclear. In this study, we compared the diversity and abundance of AOA and AOB in Beiyun River sediments from summer to winter. AOB dominated numerically over AOA and the abundance of both the amoA genes were much higher in winter than in summer, while AOA communities were more phylogenetically diverse than AOB in this study area. Phylogenetic analysis revealed that Nitrosospira sp. was the dominant AOB in summer, with Nitrosomonas sp. dominant in winter, while no specific genus was found for AOA in present study. The main pollutants and microbial communities in the sediments deriving from Yangwa Watergate were different from other sites. Clone libraries showed that a considerable percentage of amoA sequences matched closely with those from wastewater treatment plant (WWTP) systems. The seasonal change in nitrate content was significantly and positively related to the seasonal variation in amoA abundance (P < 0.05). Total nitrogen, total organic carbon, ammonium, and pH were the main environmental factors accounting for the difference in community composition of ammonia-oxidizing microorganisms in the sediments of Beiyun River. These findings suggest that effluent inputs, water gate operation, and seasonal changes might be key factors determining the abundance and distribution of AOB and AOA in the sediments of urban rivers.