Complete ammonia oxidation (comammox) bacteria can independently oxidize ammonia to nitrate, and their discovery has changed the long-term understanding of nitrification. Comammox bacteria have been found in a variety of natural environments, but there is still a lack of understanding regarding their presence in eutrophic lakes. The main purpose of this study was to investigate the diversity and abundance of comammox bacteria in a eutrophic lake and the effects of sewage discharge on bacterial abundance. Samples were taken from five areas of Lake Tangxun, China, i.e., a water chestnut (Trapa natans) area, a lotus (Nelumbo) area, a bare sediment area, a food sewage disposal area, and a domestic sewage disposal area. The diversity of comammox bacteria and the abundance of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), comammox bacteria, and anaerobic ammonia-oxidizing (anammox) bacteria were measured. Comammox bacteria were widely found in Lake Tangxun and were closely related to Candidatus Nitrospira nitrosa and Candidatus Nitrospira inopinata. The abundance of the comammox amoA gene was lower in the two sewage discharge areas (1.3 × 107 copies g−1) than in the emergent plant areas (1.75 × 108 copies g−1) and the bare sediment area (1.0 × 108 copies g−1). The abundance of the comammox amoA gene at the five sampling areas was higher than that of the AOA amoA gene and AOB amoA gene, which indicated that comammox bacteria had a growth advantage in this eutrophic lake. Comammox bacteria were found in eutrophic lake sediments, and these bacteria belonged to comammox clade A. The abundance of comammox bacteria in the two sewage discharge areas was the lowest, indicating that they could survive in eutrophic waters, but eutrophication inhibited their growth.