To tackle the growing demand for grid-scale energy storage, the ALPHEUS project proposes a novel low-head pumped hydro storage system aimed for coastal application in countries where the topography does not allow for traditional high-head storage. This system consists of a reversible pump-turbine technology with two contra-rotating runners coupled to their respective axial-flux motor-generators as well as a dedicated control, optimising for energy balancing and the provision of ancillary services. To better understand the integration and dynamic interaction of the individual components of the plant and to allow for the simulation of a wide variety of operating conditions and scenarios, this research aims at developing a system model coupling the hydraulic, mechanical and electrical components. Numerical results are compared and verified based on CFD simulations. While some inaccuracies have to be expected, the comparison shows an overall good match with only minor deviations in dynamic behaviour and steady state results.