Heavy metal concentrations and physicochemical parameters in coastal waters were measured to analyze the spatial distribution characteristics, pollution degrees, and sources of heavy metals in the heavily urbanized Guangdong-Hong Kong-Macao Greater Bay Area (GBA) in China. Heavy metal concentrations in the eastern GBA were higher than those in the west, and the levels of Pb and Zn in seawater were higher than those in groundwater and river water. Both the pollution factors and comprehensive water quality index demonstrated that seawater was not contaminated with As, Cd, Cr, and Ni, whereas low to considerable levels of contamination of Pb and Zn were observed in the central and eastern sections of the GBA. Multiple statistical analyses suggested that the Pb and Zn contaminations in seawater were probably derived from atmospheric deposition and human activities, and the excess amounts of As, Cd, Cu, Ni, and Zn in groundwater were attributed to anthropogenic activities. The heavy metal fluxes from submarine groundwater discharge (SGD) were comparable to, or even greater than, those from local rivers. Therefore, SGD is a significant invisible contributor of heavy metals into the coastal ocean that has often been overlooked in comparison to other visible pollution sources. This study suggests that SGD should be considered in the assessment of heavy metal pollution and future water quality management protocols in marine ecosystems.