Global WGM-12 gravity and EMAG2v3 magnetic models were used to present new information of the Estonian crust. The Estonian Precambrian crystalline basement, composed of Paleo-Meso Proterozoic metamorphic and igneous rocks, is covered by a Paleozoic sedimentary rock deposit 100–800 m thick. The present work aims to map structural patterns and recognise physical layers of the crust over Estonia using global potential models. The gravimetric data was used to identify the depth of the Moho and Conrad discontinuities. The magnetic data has been processed to calculate the Curie point depth (CPD), which was then used to estimate heat flow (HF) values in the study area. The depth of the Moho indicates an average value of 60 km, while the average depth of the Conrad discontinuity is around 18 Km. The depth of the CPD reveals an average value of 15 km. Different derivative techniques were applied over the residual part of both potential models, to delineate and map geophysical lineaments. The subsurface of Estonia has been divided into six petrological-structural zones: Tallinn, Alutaguse, Jõhvi, West-Estonian, Tapa and South-Estonian. Geophysical lineaments in each zone subsurface division delineates a NW-SE trend, perpendicular to the NE-SW oriented Fenno-Sarmatian collision. To visualise the anomalous crustal variations over Estonia, different profiles showing varying values of potential fields, CPD and heat flow are presented, especially around the Precambrian Rapakivi granitic plutons and in the Paldiski-Pskov deformation zone, due to the high contrast observed by mapping the different results over these areas. •A spectral analysis and modelling of the global potential fields in Estonia has been carried out.•A reconnaissance of the physical layers of the Estonian crust (i.e., Moho and Conrad discontinuities, Curie depth point) was performed.•Heat Flow tends to increase around the zones where the Elastic thickness and the Moho discontinuity are deeper, and possible fractured zones arise (i.e., deformation zones).•Potential geophysical lineaments in Estonia seem to have a tectonic significance due to the processes of the Svecofennian orogeny.