Groundwater pollution is a global issue in highly populated areas, the Eastern Nile Delta region is a typical example; especially around artificial wastewater drains. In the present work, a multidisciplinary approach using hydrogeochemical, geostatistical, microbiological and geophysical data was applied to determine the vulnerability conditions and to identify potential pathways through which contaminants could potentially percolate to shallow aquifers in the southern boundary of the Eastern Nile Delta.