Identifying the transformations of heavy metal in different media is a scientific issue, and geographical detector is applied to evaluate the spatiotemporal stratified heterogeneity mechanisms for heavy metals in the Yangtze River Estuary. Heavy metal concentrations in water and sediment were consistent with lognormal distributions. Their concentrations were organized into four classes. Class 1 included concentrations that were less than or equal to 25%, Class 2 included those between 25%–50%, Class 3 concentrations were between 50%–75% and Class 4 were >75%, which were based on their lognormal distributions. In water and sediment, the mean heavy metal concentrations yearly decreased from 2012 to 2016. The Chongming area was significantly lower than those found in the other areas, which is the least affected area by anthropogenic activities. The explanatory power of sediment to spatiotemporal stratified heterogeneity of heavy metals in shellfish organisms was much greater than that of water.
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