Substituted polycyclic aromatic hydrocarbons (SPAHs) have shown higher health and ecological risks than the corresponding parent PAHs (PPAHs) from laboratory studies, their variations in freshwater system, especially in surface sediment and pore water, remain inadequate understanding. In this study, we revealed the coexistence, ecological risk, and multiple factors affecting variations and sources of PPAHs and SPAHs (nitrated PAHs (NPAHs), oxygenated PAHs (OPAHs)) in the surface sediment-pore water system from a typical urban river in Northern China. The concentration ranges of Σ26PPAHs, Σ10NPAHs, and Σ4OPAHs in the surface sediments were 153.0–5367.4, not detected (N.D.)–105.4, and 42.2–1177.0 ng·g−1 dry weight, and fell within 0.6–38.8, N.D.–297.9, and N.D.–212.6 ng·mL−1 in the pore waters. The t-distributed stochastic neighbor embedding (SNE) coupled with the partitioning around medoids (PAM) elucidated spatiotemporal the variations in PAHs, emphasizing the impacts of industrial activities and sewage discharges. Besides the geochemical and hydrochemical conditions, SPAHs were affected by the potential secondary formation, especially during the wet season. The method comparisons indicated the advantages of principal component analysis-multivariate linear regression (PCA-MLR) and n-alkanes model on source identification. PAHs mainly originated from fossil fuel combustion and vehicular exhaust. The top risk quotient (RQ) values for PAHs occurred in the urban and industrial sections. A majority of the surface sediment samples emerged with low to moderate exposure risks, while all the pore water samples showed high exposure risks. The RQs of OPAHs were significantly higher (p < 0.01) than those of PPAHs. The results suggested the secondary formation of SPAHs as an important role in ecological risks of PAHs in the urban river system.