Underwater sonar survey using Side Scan Sonar (SSS) and Single beam Echo-sounder (SBES) was used for the investigation of the old Nubian archaeological villages buried within the bottom topography of Nasser Lake. The research objective involved emphasizing the efficiency of marine geophysical techniques in the detection of the submerged old Nubian Villages in Nasser Lake behind the High Dam, the study also aimed to study riverbed topography and determining the old course of the Nile River in the area. The resulted bathymetric maps showed that the two former banks of the Nile River in the study area were characterized by two distinct natures, while the shoreline has retreated with different extents starting from 250 m at the southern regions up to 3 km in the northern parts. The high-resolution sonar images of the bottom uncovered distinctive acoustic patterns according to difference in the returned backscatter strength. Submerged Nubian houses were detected along some areas of the eastern bank, which were found either standing over elevated rocky cliffs or built on multiple tiered levels. Precise target measurements were applied on the detected houses and different dimensions were obtained, which suggest that these houses were built according to the availability of suitable land to construct such dwellings.