Aswan area in South Egypt experiences continuous seismic activity due to seismogenic active faults, particularly Kalabsha and Seiyal active EW faults. The seismic site characterization is not properly identified, although the presence of high-density distribution of earthquake stations. The present study investigates fourteen earthquake stations of the Egyptian National Seismic Network, as well as six microtremor measurement sites. We analyzed ground motions due to seismogenic active faults recorded at surface from these fourteen earthquake stations. We measured microtremors for up to 120 min with portable seismometers at six sites in the vicinity of the High Dam area. The horizontal-to-vertical spectral ratios of earthquakes (EHVSR) and microtremors (MHVSR), their plots as a function of frequency and direction of motion, and diffuse field inversion are used in the study. Therefore, we could provide an obvious understanding of the site characterization including resonance frequencies, directional amplifications, and back-calculated subsurface velocity structures at these stations and sites. We found three predominant amplification directions of NS, EW, and NE–SW due to the horizontal components of the seismic waves. These amplification directions are near-transversal ~ transversal to the NS and EW strikes of the active fault system in the study area. In time–frequency analyses of the records, this directionality is observed clearly for S-wave and surface wave time windows. We validated the diffuse field inversion process not only using fitting between observed and inverted EHVSRs and MHVSRs, but also using available geological 2D cross sections and hydrological information in Aswan area.