The time-variation of the magnetotelluric (MT) fields was recorded at 37 measurement stations in the Thrace Basin (North-western Türkiye) by a remote-reference MT system that records the MT data in two frequency bands allowing a data acquisition between 320–7.5 Hz and 6–0.00055 Hz, respectively. The measurement stations were located from the Aegean Sea to the Black Sea seashores along a 207 km profile in the southeast-northwest direction. Three-dimensional inversion of MT data outlined the main geological elements of the region, the interface between sedimentary cover and basement rocks. The total thickness of the sedimentary layers in the basin is interpreted using the inflection and deflection points of the three-dimensional resistivity model in the vertical direction.