•Determination of peat stratigraphy, peat thickness and basin morphology.•Comparison of geophysical and conventional approaches in peatland environment.•3D model was created from GPR data to visualize the morphology.•Peatland formed from four smaller lakes which were later joined in one lake. Owing to their anoxic environment, peatlands play an important role in the preservation of records documenting past atmospheric depositions. To determine past records, data on peat stratigraphy and bog development are needed. Ground penetrating radar (GPR) was used to determine the peat thickness and morphology of the Šijec bog on the Pokljuka plateau in Slovenia, which will serve as a basis for further geochemical studies. Information on the stratigraphy below the peat/clay boundary was acquired by applying electrical resistivity tomography (ERT). The GPR results reveal four depressions within the peat bog, which are separated by elevated ridges. Within the depressions the peat reaches a depth of 6–9 m. The edges of the bog are flat, with peat thickness ranging from 2 to 4 m. The reach of the GPR was complemented with manual peat probing. A comparison of the depths obtained using GPR and the peat probe reveals that the results of both methods correspond well in most locations. The ERT indicated similar peat depths; peat responds with high electrical resistivity. In contrast, clayey sediments with low resistivity are found below the peat. The peat depressions are underlain with larger clayey depressions reaching more than 20 m in thickness and represent lake sediments. The complementary geophysical methods proved to be an efficient approach with which we can delineate the peat morphology and the underlying stratigraphy. Both indicate bog formation from a lake with four deeper depressions, that are separated by glacial deposits. The results presented here show the potential for geophysical methods to infer formational processes in peatlands, showing the presence of a series of isolated basins that later coalesced into a single peat landform. This interpretation is consistent with previous conceptual models from studies in boreal regions.