Submerged Floating Tunnels are a new type of infrastructure, still representing a challenge in structural engineering both from the theoretical and the practical point of view. In this paper some issues arisen in generating the seaquake input (transmission through water of the effects of the seabed seismic motion) for a 3D finite element analysis of Submerged Floating Tunnels are presented and discussed. This loading source has been pointed out buy preliminary analyses as an important additional hydrodynamic loading on the tunnel which can play a significant role, and thus deserves further investigations.