Coastal heavy-metal contamination poses significant risks to marine ecosystems and human health, necessitating comprehensive research for effective mitigation strategies. This study assessed heavy-metal pollution in sediments, seawater, and organisms in the Pearl River Estuary (PRE), with a focus on Cd, Cu, Pb, Zn, As, Hg, and Cr. A notable reduction in heavy metal concentrations in surface sediments was observed in 2020 compared to 2017 and 2018, likely due to improved pollution management and COVID-19 pandemic restrictions. Spatial analysis revealed a positive correlation between elevated heavy-metal concentrations (Cu, Pb, Zn, Cd, and As) and areas with significant human activity. Source analysis indicated that anthropogenic activities accounted for 63 % of the heavy metals in sediments, originating from industrial effluents, metal processing, vehicular activities, and fossil fuel combustion. Cd presented a high ecological risk due to its significant enrichment in surface sediments. Organisms in the PRE were found to be relatively enriched with Hg and Cu, with average As concentrations slightly exceeding the Chinese food-health criterion. This study identified high-risk ecological zones and highlighted Cd as the primary pollutant in the PRE. The findings demonstrate the effectiveness of recent pollution control measures and emphasize the need for ongoing monitoring and mitigation to safeguard marine ecosystems and human health.