Excessive dissolved inorganic nitrogen (DIN) added to the urban river systems by point-source inputs, such as untreated wastewater and wastewater treatment plant (WWTP) effluent, constitutes a water-quality problem of growing concern in China. However, very little is known about their impacts on DIN retention capacity and pathways in receiving waters. In this study, a spatially-intensive water quality monitoring campaign was conducted to support the application of the river water quality model WASP7.5 to the PS-impacted Nanfei River, China. The DIN retention capacities and pathway of a reference upstream Reach A, a wastewater-impacted Reach B and an effluent-dominated Reach C were quantified using the model results after a Bayesian approach for parameter estimation and uncertainty analysis. The results showed that the untreated wastewater discharge elevated the assimilatory uptake rate but lowered its efficiency in Reach B; while the WWTP effluent discharge elevated both denitrification rate and efficiency and made Reach C a denitrification hotspot with increased nitrate concentration and hypoxic environment. The effects of the point-source inputs on the DIN retention pathways (assimilatory uptake vs. denitrification) were regulated by their impacts on river metabolism. Despite different pathways, the total DIN retention ratios of Reaches A, B and C under low-flow conditions were 30.3% km-1, 14.3% km-1 and 6.5% km-1, respectively, which indicated the instream DIN retention capacities were significantly impaired by the point-source inputs. This result suggests that the DIN discharged from point-source inputs to urban rivers will be transported downstream with the potential to create long-term ecological implications not only locally but also regionally.