Metal contents, forms, risks, sources, and their correlation with organic matter in the sediments of Beijing and Wuhan were studied to assess the difference in metal pollution between northern and southern China, as well as the associated coupling mechanisms with organic matter. The contents of Cr, Cu, Ni, and Zn in overlying water in Beijing were significantly higher than those in Wuhan (p <
0.01). Conversely, the Ni content in the sediments of Wuhan was significantly higher than in Beijing (p <
0.01). Ecological risk assessments revealed that the risk potential of Cd was medium to high in both cities, while the risk index values for other metals were below 40, indicating low risk. There was no observable correlation between dissolved organic carbon (DOC) and these metals in the overlying water of Beijing, but DOC showed a positive correlation with Cd, Zn, and Pb in the overlying water of Wuhan, with correlation coefficients of 0.41, 0.52 and 0.38, respectively. In addition, dissolved organic matter in Beijing's overlying water primarily consists of visible fulvic acid, while Wuhan's consists of UV fulvic acid indicating that different molecular weights of fulvic acid can affect the behavior of heavy metals. The total organic carbon in the sediments of Wuhan was higher than that in Beijing, with humin (HM) being the predominant component of organic matter in the sediment. Fourier-transform infrared spectroscopy analysis revealed that carboxyl groups were present only in HM of Beijing. This difference in HM content between the two cities suggests that HM plays a primary role in metal migration. Furthermore, soil organic matter significantly contributes to sediment HM in Wuhan and is a key differentiator between the HM sources in the two cities. These results may serve as a valuable reference for addressing metal pollution in urban water bodies.