As transitional zones of land–sea interaction, coastal bays are increasingly exposed to anthropogenic pollution pressures, yet many assessments still rely on a single environmental medium. To help address this gap, this study developed an integrated multimedia assessment framework encompassing seawater, surface sediments, and typical marine organisms to investigate the ecological risks and potential anthropogenic drivers of potentially toxic elements (PTEs) in Sanmen Bay, a typical eutrophic semi-enclosed bay on the central coast of China. Field sampling was carried out over four seasonal cruises in 2023, and eight PTEs (Cu, Pb, Zn, Cd, Cr, Hg, As, and Ni) were quantified by ICP-MS and AFS under strict QA/QC control. The results indicate marked spatial heterogeneity, with relatively elevated clusters mainly distributed in the northwestern nearshore and inner-bay areas. Cd and Hg showed the most pronounced enrichment in sediments (mean contamination factors of 3.44 and 3.02; individual potential ecological risk indices up to 103.23 and 120.72), suggesting they are among the main ecological stressors for the regional benthic environment. By applying a combined PMF–SOM–GIS multi-model strategy to the surface sediments, the study indicates that the regional sedimentary enrichment appears to be jointly driven by natural background and anthropogenic activities. Four dominant sources were apportioned: a natural geological background slightly disturbed by agricultural non-point sources (33.3%), a mixed non-point source of fertilizer application and mariculture (15.8%), a point source of port-industrial wastewater discharge (28.7%), and a mixed source of coal combustion and shipping (22.2%). Overall, by helping to clarify the biogeochemical behaviour of PTEs in Sanmen Bay, this study offers a practical, data-driven analytical strategy for pollutant source apportionment in similar coastal ecosystems.