Two sedimentary cores in the Minjiang River estuary (SE China) are documented for grain size, clay minerals, heavy metals, magnetic parameters and Pb isotopes to investigate the source and historical variation of heavy metals. The MJK9 core was collected outside of the Minjiang River estuary, and the core is composed of mixed sediments, of which ~ 70% from the Yangtze River and 30% from the Minjiang River. It is thus difficult to be used for tracing the human activity along the Minjiang River. In contrast, the sediments of MJK16 core which was collected in a nearshore area are primarily from the Minjiang River. The enrichment factors of the sediments were < 1.5, indicating minor pollution. The results indicate that the sediments of the MJK16 core have Cu and Pb concentrations increasing since 1980, associated with the increase of magnetic mineral concentration and ²⁰⁶Pb/²⁰⁷Pb and ²⁰⁶Pb/²⁰⁸Pb of the sediments. We compared the Pb isotopic compositions between our results and those for the deposit mining in the Minjiang River basin, and aerosols and coal dust in south China, and considered that Pb in the sediments of the MJK16 core was derived primarily from weathered rocks as well as industrial emission (e.g. coal combustion). The sediments have anthropogenic Pb concentrations ranging from 6% in 1950 to 23.7% in 2010, consistent with the impact of rapid urban and industrial development in China.