Atka is a subduction-related volcanic island located in the central part of Aleutian Arc. The northeastern part of this island forms the Atka Volcanic Complex (AVC), which is built as a relict shield volcano of a circular shape overlain by several active and extinct volcanic vents of different ages. During the past few decades, two active volcanoes within AVC,—Korovin and Kliuchef—demonstrated mostly phreatic eruptions and intensive fumarolic activity. We have created the first tomographic model of the crust beneath AVC with the use of data of eight permanent stations of the Alaskan Volcanological Observatory operated in the time period from 2004 to 2017 that included arrival times of the P and S waves from local seismicity. Based on a series of checkerboard tests, we have demonstrated fair vertical and horizontal resolution of the model down to ~6 km depth. Beneath the Korovin and Kliuchef volcanoes, we have revealed two isolated anomalies of high Vp/Vs with values exceeding 2, which represent separate magma chambers that are responsible for magmatic eruptions of these two volcanoes. In shallow layers down to 2–3 km deep, we observe an alternation of zones with low and high values of the Vp/Vs ratio, which are likely associated with the circulation of meteoric fluids in the uppermost crust. Moderately high Vp/Vs anomalies indicate zones of meteoric water penetration down to the ground. On the other hand, the very low values of Vp/Vs reaching 1.5 depict the areas where meteoric water reached the hot magma reservoir and transformed into steam. On the surface, these zones coincide with the distributions of fumaroles. The outflow of these steam currents from active vents of Korovin and Kliuchef led to episodic phreatic eruptions, sometimes synchronous.