The application of zinc (Zn) isotopes in bivalve tissues to identify zinc sources in estuaries was critically assessed. We determined the zinc isotope composition of mollusks (Crassostrea brasiliana and Perna perna) and suspended particulate matter (SPM) in a tropical estuary (Sepetiba Bay, Brazil) historically impacted by metallurgical activities. The zinc isotope systematics of the SPM was in line with mixing of zinc derived from fluvial material and from metallurgical activities. In contrast, source mixing alone cannot account for the isotope ratios observed in the bivalves, which are significantly lighter in the contaminated metallurgical zone (δ66ZnJMC = +0.49 ± 0.06‰, 2σ, n = 3) compared to sampling locations outside (δ66ZnJMC = +0.83 ± 0.10‰, 2σ, n = 22). This observation suggests that additional factors such as speciation, bioavailability and bioaccumulation pathways (via solution or particulate matter) influence the zinc isotope composition of bivalves.