<p>One of the aims of project SIGHT (SeIsmic and Geochemical constraints on the Madeira HoTspot system) is to obtain a 3D model of SV-wave velocities of the crust and upper mantle of the Northeast Atlantic area encompassing Madeira and Canary Islands to the Atlas-Gibraltar zone, using seismic noise cross-correlations in the period range 2-100 s. Ambient noise cross-correlation has been successfully applied in a variety of tectonic environments to image the structure of the Earth subsurface. This technique overcomes some limitations ascribed to source&#8211;receiver geometry and sparse and irregular earthquake distribution, allowing to image Earth structure with a resolution that mainly depends on the network design. However, the effect of the water layer in the short period Empirical Green Functions, which are obtained by seismic noise cross-correlation, for interstation paths crossing the ocean is still poorly understood.</p><p>In several studies, it has been observed that the presence of water and sediments is responsible for later wave-train arrivals. Those later arrivals are frequently disregarded when measuring group velocity, either by considering only longer periods or by specifying a given velocity range.</p><p>In this work, we present a systematic study of the influence of the water layer on both vertical and radial synthetic Rayleigh waves, as well as on higher-mode conversion and on the group velocities dispersion measurements.</p><p>We show that although the fundamental mode dominates, the presence of the first overtones at short periods (typically below 8 seconds) cannot be neglected. We also show that specifying a given velocity range when retrieving group velocity can result in a mixture of modes. Our tests reveal that, at short periods, the water has a dominant effect on ocean-continent laterally varying media.</p><p>This is a contribution to projects SIGHT (Ref. PTDC/CTA-GEF/30264/2017) and STORM (Ref. UTAP-EXPL/EAC/0056/2017). The authors would like to acknowledge the financial support FCT through project UIDB/50019/2020 &#8211; IDL.</p>