The transition zone between the Southern Eastern Alps and the Dinarides is situated in western Slovenia and northeastern Italy. Here, a system of mainly NW-SE trending, right-lateral strike-slip faults accommodates the shortening between the Adriatic Plate and Eurasia. Due to the low deformation rates, geodetic techniques and seismology provide only limited insights into the activity of those faults. Geomorphological studies are confronted with problems arising from the low fault slip rates, distributed deformation, and unfavourable conditions due to the karst environment. One way to overcome these problems is the use of paleoseismology, i.e. the excavation of active faults to study their earthquake history and slip behaviour. A prerequisite for paleoseismological trenching is knowledge on the precise location of the fault trace and the availability of a suitable sediment record. We performed geophysical surveys across the potentially active faults in Slovenia and Italy to select sites for paleoseismic trenching. We used a ground-penetrating radar (GPR) system from Geophysical Survey Systems Inc (GSSI) with monostatic 100 MHz, 270 MHz, and 400 MHz antennas and a Pulse EKKO Pro Sensors & Software system equipped with bistatic 250 MHz antennas. All data were processed with the ReflexW software (Sandmeier Geophysical Research). Processing included frequency bandpass filtering, background removal, gain adjustments, and topographic corrections. The topographic data were extracted from the 1 m DEM. Electric resistivity tomography (ERT) was performed with a 4-point-light system (Lippmann Geophysikalische Messgeräte). We used up to 80 electrodes with varying electrode spacing for Wenner, Schlumberger, and Dipole-Dipole arrays, depending on target resolution and depth. Data inversion was done with Res2DInv (Geotomo Software) and included manual de-spiking and topographic corrections. Along several profiles we measured the vertical gradient of the geomagnetic field and the total magnetic field strength with a proton magnetometer GSM - 19T (GEM Systems). The system consists of a rover and a base station, which allows correcting the data for diurnal variation. Depending on the equipment used and the survey parameters, these methods allow insights into the first few metres of the subsurface with a resolution of few centimetres (georadar) to a few metres (ERT). We focussed on sites that host Quaternary sediments. Most of the data in this dataset are 2D profiles perpendicular to the mapped traces of active faults. Several promising sites were investigated in 2.5D, i.e. the profile line spacing was dense enough to compute a pseudo-3D dataset. We collected the data in May and June, 2018. This dataset contains ~2.5 km of magnetic data, ~20 km of GPR data, and ~1.7 km of ERT data. This work was undertaken for the DFG project "Earth surface response to Quaternary faulting and shallow crustal structure in the eastern Adria-Alpine collision zone and the Friulian plain" within the DFG-funded priority programme SPP2017 - Mountain building processes in 4D.