Near-coastal marine sediments often provide high-resolution records of various anthropogenic influences such as the release of heavy metals, which pose a potentially negative influence on aquatic ecosystems because of their toxicity and persistence. In places, the gradual onset of man-made heavy metal emission dates back to ~ 4500 years BP and is difficult to distinguish from potential natural sources. New Zealand offers a perfect setting for studies on anthropogenic impact due to its well-defined three-step development: pre-human era (until ~ 1300 CE), Polynesian era (~ 1300–1800 CE) and European era (since ~ 1840 CE). However, hardly any information exists about the degree of heavy metal input to New Zealand’s coastal areas and the ‘pristine’ natural background values. This study determines the natural background contents of lead (Pb) and zinc (Zn) in marine sediments of the Firth of Thames, a shallow marine embayment on New Zealand’s North Island, and investigates anthropogenic inputs in historic times. Eight sediment cores were analysed by X-ray fluorescence (XRF) for their element composition and temporally resolved by a pollen and radiocarbon-based stratigraphic framework. Sharp increases in Pb and Zn contents occurred simultaneously with the onset of goldmining activities (1867 CE) in the nearby catchment area. The contents of Zn (Pb) increase from very stable values around 60 (13) ppm in the older sediments, interpreted to reflect the natural background values, to an average maximum of 160 (60) ppm near the core top, interpreted to reflect a significant anthropogenic input. These findings unravel the history of contamination in the Firth of Thames and provide an urgently needed database for the assessment of its current ecological state.