This work intends to identify pollution sources along the margins of Guanabara Bay (GB; SE Brazil) through a multiproxy approach and Bayesian stable isotopic mixture model (BSIMM). For this purpose, 33 surface sediment samples were collected and analyzed for granulometry, geochemistry (heavy metals, total organic carbon-TOC, stable isotopes of carbon and nitrogen-δ13C and δ15N, Rock-Eval pyrolysis parameters-REPP), and physicochemical parameters. Metal concentrations (E) dissolved in water (EW), adsorbed by organic matter (EOM) and by Mn hydroxides (EMn), and total extracted concentrations (ET) were analyzed. Sampling was conducted in 2018 after an oil spill from Reduc Oil Refinery. Potential Ecological risk index (PERI), based on metals, classified 85% of the analyzed stations as having moderate to considerable ecological risk. The metals with the potential to cause the highest ecological risk were CdW, CdOM, PbOM, and HgOM. The combination of BSIMM and REPP data was an effective proxy for oil spill detection by indicating the presence of polycyclic aromatic hydrocarbons (PAHs). Relatively high TOC contents suggested that the analyzed stations are eutrophicated environments. BSIMM discriminated three groups of stations with different sources of organic matter (OM), endorsing the result previously shown by the cluster analysis: (A) Niterói region, Botafogo marina, Glória marina, Fiscal and Fundão islands with diffuse sources of OM, including marine phytoplankton and material of continental origin from highly polluted rivers and domestic sewage; (B) region near Fundão and Governador islands and Mangue Channel outlet with OM (≃70%) supplied by highly polluted streams and a small contribution of PAHs; (C) Duque de Caxias and Botafogo-Urca inlet with significant contributions of PAHs, materials from C-3 plants and rivers polluted by urban sewage. Results of linear regressions in conjunction with BSIMM indicate that HgMn and PbOM mainly affect Group A's stations. Although the eastern margin of GB (Niterói; Group A) showed greater oceanic interaction than the other groups, it presented substantial concentrations of metals, potentially harmful (i.e., Hg and Pb) to marine biota and human health.