El Laco is part of the Cordón de Puntas Negras sector of the Central Volcanic Zone,:681,682 directly south of that volcanic chain. It sits atop a quartzite and sandstone basement that was lifted from the seaground during the Acadian orogeny and is of Ordovician age. Later, Mesozoic and Cenozoic sedimentation occurred, which was then buried by Tertiary rhyolites.:681,682 Two major volcanic lineaments cross in the El Laco area, including the so-called Calama-Olacapato-El Toro lineament. El Hueso volcano to the north is high and has a basement diameter of . It has a crater with a diameter of .