Excessive dissolved inorganic nitrogen (DIN) added to urban river systems by point-source (PS) inputs, including raw sewage and wastewater treatment plant (WWTP) effluent, constitutes a water-quality problem of growing concern worldwide. However, the quantification of their impacts on DIN retention capacity and pathways in receiving water still remains partial. In this study, a spatially intensive water quality monitoring campaign was conducted to support the application of a water quality model to a PS-impacted urban river in Hefei City, China. The DIN retention capacities and pathway of a reference upstream Reach A, a raw-sewage-impacted Reach B and a WWTP-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 raw sewage discharge elevated the assimilatory uptake rate but lowered its efficiency in Reach B, while the WWTP effluent discharge elevated both the denitrification rate and efficiency and made Reach C a denitrification hotspot with an increased nitrate concentration and hypoxic environment. The effects of the PS 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 that the instream DIN retention capacities were significantly impaired by the PS inputs. This result suggests that the DIN discharged from PS inputs to urban rivers will be transported with the potential to create long-term ecological implications not only locally but also more distant downstream.