In this study, we analyse both ground gravity and aeromagnetic data in order to delineate structural trends, fault systems and deduce sedimentary thicknesses within the Ajdabiya Trough in Libya’s northeast. A high-pass filter and a reduced-to-the-pole (RTP) transformation are applied to the gravity and aeromagnetic data respectively. Different filters are used to enhance the structural signatures and fault trends within the study area. The Werner deconvolution and source parameter imaging (SPI) techniques are applied to the RTP magnetic data for source depth estimation. Four well-data within the area are used as constraints in the two-dimensional forward modelling process. The results show that the Ajdabiya Trough is characterised by gravity anomaly highs and magnetic anomaly lows. The analysis of gravity data shows predominant Northeast–Southwest structural trends, whereas the analysis of magnetic data shows predominant North–South magnetic lineaments within the Ajdabiya Trough. The Euler deconvolution depth estimates of faults depths range between 1500 and 9500 m. The SPI estimates of the magnetic basement range between 2500 and 11,500 m beneath the study area (deepest beneath the Ajdabiya Trough). Constrained by the well-data, six major layers characterize the four profiles that are taken within the area. One of the profiles shows a high-density intrusion (about 4 km from the surface) within the sedimentary sequence. The intrusion may be the result of the rifting Sirt Basin which caused a weakening of the crust to allow for mantle intrusion.