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Zinc stable isotopes (δ⁶⁶Zn) serve as a widely fingerprinting tool for detecting anthropogenic Zn contamination. However, there is a limited understanding of δ⁶⁶Zn behavior during the sorption of Zn to minerals and organic matter. In this study, we have determined the δ⁶⁶Zn values in specific fractions to investigate their effectiveness in tracing anthropogenic Zn. The revised Community Bureau of Reference (BCR) extraction procedure was applied to a coastal marine core from Osaka Bay and from a lacustrine core from Lake Biwa, both with a history of anthropogenic metal pollution. The δ⁶⁶Zn values varied from −0.14 ‰ to +1.00 ‰ across the four to five chemical fractions with up to 0.9 ‰ variation within a single horizon. The highest δ⁶⁶Zn values in the acid-soluble fraction (up to +1.00 ‰) could be explained by the preferential sorption of ⁶⁶Zn to carbonates and/or the preferential incorporation of ⁶⁶Zn into calcite. The complex isotopic fractionation during the sorption of Zn to and co-precipitation with Fe–Mn oxyhydroxides likely resulted in an unclear pattern of the δ⁶⁶Zn values of the reducible fraction. Low δ⁶⁶Zn values in the oxidizable fraction (Osaka Bay) agree with the ⁶⁴Zn enrichment in phytoplankton. Higher δ⁶⁶Zn values of the reducible and oxidizable fractions of the Lake Biwa core indicate that environmental conditions (e.g. ionic strength) and for instance different phytoplankton species or dissolved and suspended particulate matter input drive the Zn isotope fractionation depending on the system (marine vs. lacustrine). The δ⁶⁶Zn values of the acid-soluble fraction (Osaka Bay and Lake Biwa), of the reducible fraction (only Lake Biwa) and of oxidizable fraction (only Osaka Bay) better reflected the temporal changes in the Zn concentration than the bulk sediment, indicating that these fractions could be a sensitive fingerprinting tool for anthropogenic Zn contamination.