This paper presents the development of an urban river water quality model which considers the physical-biochemical processes within rivers and the incorporated urban catchment rainfall-runoff process developed with the time–area method. Unlike other models that simulate the hydrological and receiving water quality processes in the rural areas of the watershed scale, the model developed here is typically efficient for simulating the water quality response to nonpoint loadings from urban drainage systems, where the hydrological process is disturbed by artificially pumped discharge in wet-weather periods. This model is employed to assess the river water quality restoration in Nanfei River in Hefei City, China, where the model is calibrated against the measured data (i.e., the COD, the BOD5, the NH3-N, and the DO) in 2010, and the model parameters are suggested. It is shown that the nonpoint pollutants from the urban catchments contribute 34%-47% of the total pollutant inputs (i.e., the COD, the BOD5, and the NH3-N), despite their low flow component of 13.4%. Apart from the improvement of the wastewater treatment plant effluent (i.e., Grade IV of the Surface Water Quality Standard), a nonpoint loading reduction of 27.2%, 25.1%, and 35.3% of the COD, the BOD5, and the NH3-N are anticipated to meet the designated surface water quality standards of Grade V.