To explore the pollution sources and contribution rate of urban eutrophication lakes, a typical eutrophic lake (Lake Houguanhu in Wuhan) in the Yangtze River Basin was selected for research. With the field-measurement method, the mean-concentration method and the pollution-discharge-coefficient method, the external pollutant sources (including point source and non-point source) of Lake Houguanhu was analyzed. Non-point sources (NPS) were further divided into several source types, such as the pollutants from the rural life, the agricultural planting, the aquaculture, the livestock, the poultry farming and the urban runoff. Results show that the COD in Lake Houguanhu is mainly from the point source with a contribution rate of 54%, total phosphorus is mainly from the non-point sources with a rate of 71%. Further exploring the main non-point sources, it is found that the total phosphorus is mainly from the agricultural planting and aquaculture, with the contribution rates of 41% and 30%, respectively. The largest contribution of COD, ammonia nitrogen and total nitrogen in NPS is urban runoff, with contribution rates of 61%, 53% and 37%, respectively. For administrative districts, the highest contribution rates of COD, ammonia nitrogen, total nitrogen and total phosphorus emissions are Zhuankou Street Office (25.24%), Caidian Street Office (23.28%), Yongfeng Street Office (24.04%) and Daji Street Office (26.15%). Results indicated that, with point source treatment of the Zhuankou Street and the Yongfeng Street, the COD and ammonia nitrogen loads can be effectively reduced. The agricultural non-point source pollution prevention and control of Daji Street is the focus of total phosphorus management in Lake Houguanhu Basin.