Due to the penetration of stochastic low-carbon sources of production, requirements for flexible generation increase. The flexibility of pumped storage hydropower plants in pump mode can be improved by implementing hydraulic short circuit modes, which consists in operating the turbine(s) and the pump(s) in parallel. This new operating mode can be investigated by computational fluid dynamics to determine the head losses and to investigate the flow topology. Nine geometries of the Grand’Maison and Forces Motrices Hongrin-Léman (FMHL/FMHL+) plants are considered. Due to the lack of measurements, simulations are performed using different turbulence models and meshes to assess the uncertainty of the results. A statistical analysis of the results shows that low values of the head loss coefficients are obtained for geometries that limit the impingement of the flow on the walls and the development of a swirling flow downstream. Such geometries have the benefit of also limiting the wall pressure fluctuations and wall shear stresses, i.e. the risk of cavitation and the abrasion of the pipe walls due to sediment transport. These new results for the hydropower community are valuable for owners in implementing hydraulic short circuit mode in existing power plants or in designing new suitable junctions.