Asian megacities have severe pollution problems in both coastal and urban areas. In addition, the groundwater potential has decreased and land subsidence has occurred because of intensive groundwater pumping in urban areas. To prevent the adverse effects of urbanization on groundwater quality, it is necessary to confirm the changes in groundwater flow and contaminant transport caused by urbanization. We examined the effects of urbanization on contaminant transport in groundwater. The research areas were located around Bangkok, Thailand, and Jakarta, Indonesia, cities with populations of approximately 8 and 12 million, respectively. Each metropolitan city is located on a river delta and is adjacent to a bay. We measured the water level and collected water samples at boreholes at multiple depths (100 to 200 m) in 2004 and 2006 in Bangkok and Jakarta, respectively. The current hydraulic potential is below sea level in both cities because of prior excess abstraction of groundwater. As a result, the direction of groundwater flow is now downward in the coastal area. The Cl(-) concentration and delta(18)O distributions in groundwater suggest that the decline in hydraulic potential has caused the intrusion of seawater and shallow groundwater into deep groundwater. Concentrations of Mn and NO3(-)-N in groundwater suggest the intrusion of these contaminants from shallow to deep aquifers with downward groundwater flow and implies an accumulation of contaminants in deep aquifers. Therefore, it is important to recognize the possibility of future contaminant transport with the discharge of deep groundwater into the sea after the recovery of groundwater potential in the coastal areas.