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Osaka Bay adjacent to the Kyoto–Osaka–Kobe metropolitan area was affected by severe metal pollution during the twentieth century; yet little is known about the trace metal sources and pre-industrial human activities. We have determined the elemental concentrations and zinc stable isotope ratios (δ⁶⁶Zn) in bulk sediments and the trace metal concentrations in chemical fractions of a 9-m-long sediment core from Osaka Bay. Our goals were (1) to reconstruct the historical trace metal contamination, and (2) to identify anthropogenic Zn sources and the solid phases of anthropogenic trace metals. The core provided a continuous environmental record of the last 2300 years based on radiocarbon dating of molluscan shells. Copper, Zn, and Pb showed an initial enrichment from the 1670s AD, which could be caused by human activities due to an increasing population. In agreement with previous findings, the trace metal concentrations slightly increased from the 1870s, strongly increased from the beginning of the twentieth century, and peaked around 1960 before environmental pollution control laws were enacted. Increasing trace metal concentrations in the acid-labile and reducible fractions obtained by the Community Bureau of Reference (BCR) sequential extraction procedure toward the surface indicate carbonates and Mn oxyhydroxides were the primary fractions for anthropogenic trace metals. The δ⁶⁶Zn values (1) were constant until the 1940s, suggesting that the average δ⁶⁶Zn of industrial sources was indistinguishable from that value of the natural background, (2) showed a slight decrease from the 1950s and remained constant until the present, and (3) fell in a binary mixing process between a lithogenic (~ + 0.27‰) and an anthropogenic endmember (~ + 0.17‰), the latter likely representing a mixture of various Zn sources such as road dust, tire wear, industrial effluents, and effluents from wastewater treatment plants. We conclude the combination of Zn stable isotopes together with chemical fractions obtained by the BCR method represents a promising approach to assess the trace metal sources and their potential mobility in sediment cores from anthropogenically affected coastal areas.