Esrum Sø, with a marked elongation trending N–S, located in the glaciomorphological landscape of north-eastern Sjælland, is one of the biggest lakes in Denmark. The lake is shaped as a large ‘sink’ with steep sides and a maximum depth of c. 22 m. The present investigation and mapping of the structures of the lakebeds is based on the interpretation of 10 reflectors on 82 acquired high-resolution seismic sections (Chirp III) and correlation to the 8.5 m long Esrum Sø drill core in the northern part of Esrum Sø. A new formation, the Esrum Formation, with two members, the Fredensborg and Nødebo Members, is erected based on the geological information obtained from the drill core, and traced on the seismic sections over the major part of Esrum Sø. In the northern part of the lake, the seismic sections reveal a number of anti- and synform structures, which we group into five architectural features. The mapping of these structures show N–S trending vertical fractures, fault scarps and fold crests, which in places are bent towards a NW direction. In some, mainly southern, parts of the lake, gas stored in the gyttja (Nødebo Member) and close to the lake floor degrades the seismic signal significantly. The gas is ascribed to seepage and production close to the lake floor. The integration of the seismic interpretation and the Esrum Sø drill core data shows that the Young Baltic till constitutes the base of the depression where Esrum Sø is located. In Bølling to Preboreal time the Esrum Sø was a shallow freshwater lake with no tectonic activity (Fredensborg Member), and the major deformation and subsidence of the lake basin took place in Boreal to Atlantic time (Nødebo Member). Our interpretation favours a model of a Postglacial pull-apart basin related to extension in the wrench-fault tectonic zone aligned with the Sorgenfrei–Tornquist Zone.