Hydrogeophysical characterization using the transient electromagnetic method (TEM) and the DC resistivity sounding (VES) method was implemented in the central part of Azraq Basin (Qa Basin), Jordan, to identify and map the spatial distribution of shallow fresh and saline groundwater in the upper aquifer systems. The alluvium (Al) and chert limestone (URC) shallow aquifers show different degrees of groundwater salinization. The range of groundwater resistivity varies from 0.06 to 10.8 ohm-m. Saline groundwater was detected at depths between 5 to 30 m where the aquifers have a wide spectrum of resistivity values from 0.14 to 120 ohm-m. The integrated geophysical and hydrogeologic models are significantly correlated in chloride concentration, groundwater resistivity, and aquifer resistivity. Using 1D inversion results from the TEM and VES soundings in addition to quasi-3D modeling (1D spatially constrained inversion) at selected TEM sites, groundwater resistivity variation was attributed to two different salinization mechanisms. First, the spatial distribution of the salt content in mud flat deposits had a significant effect on the groundwater salinity. Second, in situ dissolution of near-surface rock-forming salts occurred at areas away from the mud flat deposits. The proposed hydrogeophysical models revealed the potential effect of both mechanisms in the study area.