The so-called ‘Tunguska Event’ refers to a major explosion that occurred on 30 June 1908 in the Tunguska region of Siberia, causing the destruction of over 2000 km2 of taiga, globally detected pressure and seismic waves, and bright luminescence in the night skies of Europe and Central Asia, combined with other unusual phenomena. The ‘Tunguska Event’ may be related to the impact with the Earth of a cosmic body that exploded about 5–10 km above ground, releasing in the atmosphere 10–15 Mton of energy. Fragments of the impacting body have never been found, and its nature (comet or asteroid) is still a matter of debate. We report results from the investigation of Lake Cheko, located ∼8 km NNW of the inferred explosion epicenter. Its funnel-like bottom morphology and the structure of its sedimentary deposits, revealed by acoustic imagery and direct sampling, all suggest that the lake fills an impact crater. Lake Cheko may have formed due to a secondary impact onto alluvial swampy ground; the size and shape of the crater may have been affected by the nature of the ground and by impact-related melting and degassing of a permafrost layer.