Haizhou Bay, a semi-enclosed key aquaculture area in East China, has had relatively limited research focused on trace metals and perfluoroalkyl acids (PFAAs) in its biota. This study characterized the distribution, biomagnification and health risks of selected trace metals and PFAAs in various marine organisms from Haizhou Bay. Among the species examined, zinc (Zn) was the most prevalent metal, followed by copper (Cu) and chromium (Cr), whereas cadmium (Cd), total mercury (THg), and methylmercury (MeHg) contents were relatively low. Perfluorooctane sulfonate (PFOS) was the most abundant PFAA, followed by perfluorooctanoic acid (PFOA). The calculated trophic magnification factors (TMFs) were above one for Cr, THg, MeHg, and all PFAAs except perfluorobutanoic acid (PFBA) and perfluorotetradecanoic acid (PFTeDA). Across animal groups, gastropods exhibited relatively low levels of THg, MeHg, and perfluorosulfonic acids (∑PFSAs). By comparison, fish generally had lower levels of Cd and Cu compared to other animal groups, and demersal fish had significantly higher MeHg compared to gastropods. Certain organisms, such as cephalopods and shrimps, were found to pose potential health risks due to elevated levels of Cd, while levels of other studied metals, PFOS and PFOA generally appeared to be within safe limits for human consumption. Further research is needed to assess the sources and impacts of these and other contaminants.