There are two low-enthalpy geothermal systems along the eastern border of the United Arab Emirates: Ain Khatt (Khatt City, Ras Al Khaimah Emirate) and Green Mubazzarah–Ain Faidha (GMAF) (Al-Ain City, Abu Dhabi Emirate). The hot springs are likely to be meteoric waters fed through deep-seated faults that intersect the geothermal reservoirs at 2.6–3.8 km depth. Gravity and magnetic data were analyzed by gradient (horizontal derivative “HD”, and improved normalized horizontal tilt angle “INH”), and separately 3D modeled to image the subsurface structure of the two UAE geothermal systems. Bouguer anomalies in GMAF and Ain Khatt range from − 14.2 to 8.09 mGal and − 169.3 to − 122.2 mGal, respectively. Magnetic intensities in GMAF and Ain Khatt vary from 39,327 to 44,718 nT and 43,650 to 44,653 nT, respectively. The UAE hot springs (GMAF and Ain Khatt) are located in mainly high HD and INH regions, which reflect significant discontinuities in the basement rock, such as faults or lithological contacts. A joint inversion of magnetic and gravity data, through Artificial Neural Network (ANN) modeling, was performed to explore and interpret the 3D density and magnetic susceptibility variations. Results show that the hot springs in both geothermal systems are associated with intersecting geological contacts and fault zones. The Green-Mubazzarah–Ain Faidha hot springs may be connected at depth.