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A part of the heavy metals in estuary and coastal zone occurs naturally in the environment; the other part is due to human activity; so the directly measured concentration of heavy metal does not automatically indicate anthropogenic enrichment. Fe2O3 was used in this study as conservative tracer to distinguish natural components from anthropogenic components of heavy metal sediment concentration in the Zhujiang estuary. Compared with clay and Al2O3, Fe2O3 is more suitable as reference element. The final results showed that two zones in the Zhujiang estuary were seriously contaminated by heavy metals. One nearby the Humen mouth; the other around the west coast of the estuary. The horizontal distribution of heavy metals indicates that Zn, Ni and Cu have wider contaminating areas than TiO2, V and Cr in the estuary.