Excessive nutrient input from urban areas increases the occurrence of eutrophication. Control of nutrient loads is perceived as the primary restoration method. Quantifying temporal variation of nutrient loads is essential to understand the dynamic relationships of nutrient source-impacts in the urban water system and investigate the operational efficiency of treatment facilities for eutrophication control. Here, a holistic approach was developed to estimate nutrient loads from different sources and evaluate nutrient impacts on the urban water environment. An integrated catchment model of nutrient loads was built and applied to calculate river nutrient loads from untreated rainfall runoff, untreated sewage, and treated recharge into the eutrophic Dianchi Lake from an urban river catchment with limited infrastructure. Nutrient impacts on the lake were evaluated and a load reduction strategy was given a hint to reduce nutrient impacts of urban rivers. During the study period 2014–2016, nutrient loads from the urban river generally decreased except during heavy winter rainfall events and high-intensity pollution events associated with rainfall runoff. The average contribution of annual nutrient loads to the lake capacity indicated the underestimation of nutrient impacts of urban rivers. This approach provides new insights into urban water management and underscores the importance of sewage infrastructure.