Chongming Island is located in the lower Yangtze Estuary in China. Due to the Leachate from a refuse landfill and the hydrodynamics of the Yangtze Estuary, the groundwater environment is particularly complicated on Chongming Island. Field observations were carried out around the landfill disposal site. The groundwater table, temperature, pH, salinity, and dissolved oxygen were measured in the field by portable equipment, and 192 water samples were collected at eight groundwater sites and one surface water site. Through laboratory analysis we found the highest measured concentration of Cr to be 54.07 μg/L, and the measured concentration of Zn was in the range of 8 μg/L to more than 200 μg/L, which were both higher than their background values. Strong correlations were found between the heavy metal (Cr, Ni, Cu) concentrations and physico-chemical characteristics (salinity and pH), which indicated that both the landfill and the tides played an important role in the distribution of heavy metal concentrations. Both the HPI and PoS Indices were greater than their critical values near the disposal site, indicating groundwater pollution by heavy metals. We show that Cr and Ni are the major heavy metals causing groundwater contamination in the study region.