Pb and Cd accumulation in riparian soils and river sediments in river basins is a challenging pollution issue due to the persistence and bioaccumulation of these two trace metals. Understanding the migration characteristics and input sources of these metals is the key to preventing metal pollution. This study was conducted to explore the contents, geochemical fractionation, and input sources of Pb and Cd in riparian soils and river sediments from three lower reaches of the Pearl River Delta located in the Guangdong-Hong Kong-Macao Greater Bay Area. The total concentration of all Pb and Cd values exceeded the background values to varying degrees, and the exchangeable fraction of Cd in riparian soils and river sediments accounted for the largest proportion, while that of Pb was dominated by the residual fraction. Geoaccumulation index calculations showed that in the riparian soils, the average accumulation degree of Pb (0.52) in the Beijiang River (BJR) was the highest, while that of Cd (2.04) in the Xijiang River (XJR) was the highest. Unlike that in riparian soils, the maximum accumulation of Pb (0.76) and Cd (3.01) in river sediments both occurred in the BJR. Furthermore, the enrichment factor results also showed that Pb and Cd in the riparian soils and river sediments along the BJR were higher than those in the XJR and Dongjiang River (DJR). The relationship between enrichment factors and nonresidual fractions further proved that the enrichment factors of Cd were significantly correlated with the nonresidual fractions of Cd, which may imply various anthropogenic sources of Cd in the three reaches. Moreover, source identification based on principal component analysis (PCA) and Pb isotope ratio analysis indicated that riparian soils and river sediments have inconsistent pollution source structures. The PCA results showed that Pb and Cd were homologous inputs in the DJR, and there were significant differences only in the riparian soils and river sediments. Pb isotope tracing results further showed that the bedrock of high geological background from upstream may be the main reason for Cd accumulation in the XJR. However, the ultrahigh accumulation of Cd in the BJR is mainly caused by the input of the upstream mining and metallurgy industry. The control of upstream input sources will be the key to the prevention of trace metal pollution in these regions.