Studies have investigated heavy metal (HM) contamination in the Bohai Sea, but primarily in seawater and associated sediments, or in single rivers. For the first time, 31 major rivers discharging into the Bohai Sea were analyzed, along with 27 uniformly distributed coastal seawater samples and selected invertebrates. The elements measured were As, Cd, Cr, Cu, Ni, Pb, V, and Zn. We calculated the ‘geo-accumulation index’, the ‘metal enrichment factor’, and the ‘contamination factor’, coupled with the ‘pollution load index’, and our findings suggested low-grade HM pollution, although two conspicuous associations of elements were found to stand out in particular: One is a combination of As, Cu, Cr, and V in seawater samples that may indicate pollution from intensive ship traffic. The other shows a significant pattern of Cr, Pb, and Zn in water samples from rivers discharging between Yantai and Weihai on the Shandong Peninsula at the south edge of the Bohai Sea. This is primarily a farming area, with a moderate share of industrial enterprises. Investigations including fertilizers and pesticides point to agricultural practices and textile printing/chrome tanneries as the causes of contamination. Overall, a significant decline was found in the HM load in the rivers, apart from those discharging into the Yellow Sea section.