Transient ElectroMagnetic (TEM) sounding and Ground ElectroMagnetic (GEM) profiling have been conducted at Hawara archeological area, El Fayoum, Egypt to investigate the subsurface water and its effect on the archeological targets at this area. This archeological site comprises Hawara pyramid, the northern necropolis and a southern mortuary complex called “labyrinth”. Nowadays Hawara area is entirely abandoned and surrounded by cultivated areas, as well as, a surface water canal named “Bahr Wahba”. The surface and underground water bodies have negative effects on the foundation of Hawara pyramid and the labyrinth site, where the entrance of the pyramid is today flooded to a depth of about 6 meters below the ground surface. TEM data have been acquired at three sites in this area comprising the cultivated land, the pyramid and the labyrinth, while the GEM survey was conducted inside the labyrinth site. Integrated interpretation of these data sets indicates that, the agricultural activities and the flooding irrigation system applied to the planted area are the main sources for the water that invades the subsurface section at this area. Moreover, the subsurface water level has been recorded at variable depths ranging from 2 to 7 m below the ground surface according to the measuring site and surface elevation.