The 1982 explosive eruptions of El Chichón volcano (Chiapas, Mexico) destroyed the inner dome and created a 1-km-wide and 180-m-deep crater within the somma crater. A shallow hydrothermal system was exposed to the surface of the new crater floor and is characterized by an acid crater lake, a geyser-like Cl-rich spring (soap pool), and numerous fumarole fields. Multiple geophysical surveys were performed to define the internal structure of the volcanic edifice and its hydrothermal system. We carried out a high-resolution ground-based geomagnetic survey in the 1982 crater and its surroundings and 38 very low frequency (VLF) transects around the crater lake. A 3-D inversion of the ground-based magnetic data set highlighted three high-susceptibility isosurfaces, interpreted as highly magnetized bodies beneath the 1982 crater floor. Inversion of a digitized regional aeromagnetic map highlighted four major deeply rooted cryptodomes, corresponding to major topographic highs and massive lava dome outcrops outside and on the somma rim. The intracrater magnetic bodies correspond closely to the active hydrothermal vents and their modeled maximum basal depth matches the elevation of the springs on the flanks of the volcano. Position, dip, and vertical extent of active and extinct hydrothermal vents identified by VLF-EM surveys match the magnetic data set. We interpret the shallow lake spring hydrothermal system to be mostly associated with buried remnants of the 550 BP dome, but the Cl-rich soap pool may be connected to a small intrusion emplaced at shallow depth during the 1982 eruption.