A new method consisting of enrichment factor (EF) determination, nonmetric multidimensional scaling (NMS), and the geographic information system (GIS) technique was firstly developed to identify anthropogenic heavy metal sources in marine sediments of Hong Kong. Firstly, the EF was determined to differentiate between heavy metals originating from human and natural sources. Subsequently, NMS was applied to identify various source patterns of heavy metals, and the NMS score was calculated and spatially interpolated using GIS technology to evaluate the spatial influences of anthropogenic impacts in different areas. The concentrations of heavy metals in sediments of Hong Kong substantially exceeded their background values, demonstrating anthropogenic pollution. Two different types of human sources could be identified via NMS, one representing the industrial pollution discharges in the period from the 1960s to the 1980s before pollution control was introduced and one representing sewage discharge before the Tolo Harbour Action Plan in the mid-1980s.