Shear wave velocities of the sediment fill of a deep Alpine valley are estimated from ambient noise recorded on linear and circular arrays. We propose a combined inversion of 2‐D resonance frequencies identified from site‐to‐reference spectral ratios and Rayleigh wave dispersion curves obtained from frequency‐wavenumber analysis. The method is tested on synthetic noise data and on noise recorded at three sites in the Rhône valley in Southern Switzerland. Previous studies have shown that 2‐D resonance dominates the ambient vibration wavefield at low frequencies at the investigated sites. Inversion techniques which assume that the noise wavefield consists mainly of horizontally propagating surface waves will, therefore, fail to resolve shear wave velocities at depths below around 500 m. We show that standard techniques lead to an overestimation of shear wave velocities at depth when applied to synthetic and observed ambient noise. The combined inversion is able to resolve the shear wave velocities in the initial velocity model when applied to synthetic noise records. Application of the method to observed ambient noise improves resolution at depth and yields realistic shear wave velocities for the lower part of the sediment fil