We introduce a physically relevant stochastic representation of the rotating shallow water equations. The derivation relies mainly on a stochastic transport principle and on a decomposition of the fluid flow into a large-scale component and a noise term that models the unresolved flow components. As for the classical (deterministic) system, this scheme, referred to as modelling under location uncertainty (LU), conserves the global energy of any realization and provides the possibility to generate an ensemble of physically relevant random simulations with a good trade-off between the model error representation and the ensemble’s spread. To maintain numerically the energy conservation feature, we combine an energy (in space) preserving discretization of the underlying deterministic model with approximations of the stochastic terms that are based on standard finite volume/difference operators. The LU derivation, built from the very same conservation principles as the usual geophysical models, together with the numerical scheme proposed can be directly used in existing dynamical cores of global numerical weather prediction models. The capabilities of the proposed framework is demonstrated for an inviscid test case on the f-plane and for a barotropically unstable jet on the sphere.