The occurrence and migration of heavy metal in coastal aquifer incorporating tidal effects were investigated in detail by the field geological survey and observation. The continuous groundwater sampling, field observation (for groundwater potentiometric surface elevation, pH, dissolved oxygen, temperature, and salinity), and laboratory analysis (for Cr, Ni, Cu, Zn, Cd, and Pb concentration) were conducted through eight monitoring wells located around the landfill in the northern part of Chongming Island, China. The results showed that the unconfined aquifer medium was estuary-littoral facies deposit of Holocene, mainly gray clayey silt and grey sandy silt, and the groundwater flow was mainly controlled by topography condition of the aquifer formation strike. The background values of Cr, Ni, Cu, Zn, Cd, and Pb in Chongming Island were 3.10 ± 3.09, 0.81 ± 0.25, 1.48 ± 1.09, 43.32 ± 33.06, 0.08 ± 0.16, and 0.88 ± 1.74 μg/L, respectively. Compared with the groundwater samples around the study area, the drinking water was qualified and was free from the seawater intrusion/estuarine facies contaminant encroachment. Pollutant discharge was reflected in water quality parameters, the Cr and Cu concentrations elevated to the peak of 50.07 and 46.00 μg/L, respectively, and meanwhile specific migration regularity was embodied in observation time series as well as other elements. This migration regularity was not fully identical according to correlations between these analyzed elements. Ambient watery environment, anthropogenic disturbance, regional hydrogeological condition, and biogeochemical reactivity on heavy metals reduced/altered the significance of elements correlation in the migration pathway in coastal aquifer.