In this study, we determine the properties of the maar volcanic structure using ambient vibration analysis. We performed several ambient vibrations surveys at Mýtina maar (West-Bohemia, Czechia) to map amplification by site-to-reference spectral ratios and to estimate average shear wave velocities by array methods. As the maar diatreme is formed by a deep concave body of broken rock, strong 3D resonances develop. The site-to-reference amplification factors reach a value of 20 in the central part of the maar. Using the noise data, we demonstrate possibility of mapping the lateral dimensions of the maar infills by ambient noise measurements. To understand these observations, we developed a simplified 3D viscoelastic velocity model and simulated synthetic ambient vibrations by the finite difference method. The simulated response fitted both, measured fundamental frequencies and the amplification levels. The maximum depth of the crater was estimated to be at least 800 m.