A geotechnical and geophysical campaign was performed at sites located in the alluvial plain of the river of Beirut (Lebanon), which is characterized by a significant lateral and vertical geological variability, along with anthropogenic disturbances in the first metres. The method combination has allowed detecting a shallow conductive low velocity layer of varying depth and thickness, corresponding to a soft clay layer embedded in coarser formations. This layer was found to exert strong control on the experimental dispersion curves (estimated from both active and passive experiments) characterized by a continuous mode superposition at high frequency, associated with an increase in phase velocity. Vs profiles in boreholes turned out to be of prime importance for adequately defining the parametrization before inversion and for ensuring the reliability of the inversion dispersive estimates at low frequency. A major output of this study is also to show that this low velocity layer, along with the strong shear velocity contrast at its bottom, significantly contributes to the site seismic response, and could make it difficult to use the measured H/V peak frequency as a proxy for the soil thickness over bedrock.