The rail link between Geneva Cornavin Station, Eaux-Vives Station and Annemasse (CEVA) is currently under construction including a cut-and-cover tunnel built by slurry walls located in the alluvium of the Foron River. The covered trench cuts the groundwater table flow which causes a rise of the water table on one side of the tunnel. Thirty wells were built in order to convey water from the aquifer on one side of the tunnel to the other. For each well, traditional pumping has been replaced by a self-priming multiphase siphon in order to lower energy costs. The operating principle of the system is based on the sustaining of a free-surface vortex flow in a vacuum chamber. In this way, the multiphase siphon is primed to allow water to be transferred from either side of the tunnel. A physical model of the conveyance system has been constructed at a scale of 1:1 in order to avoid scale effects from the presence of air water mixture and due to the free-surface vortices sensitivity to scaling, particularly in a vacuum atmosphere. In this study, the results from the physical model are used to validate a Smoothed Particle Hydrodynamics (SPH) numerical simulation of the complex flow conditions. The DualSPHysics code is employed and the results presented herein regarding the depth discharge relationship are encouraging for further application in vortex flows and such devices where conventional Eulerian modelling approaches can be challenging. As far as the authors are aware, this is the first application of SPH in simulating vortex chamber flows and the result bodes well for further application in this area.