A stochastic flow representation is considered with the Eulerian velocity decomposed between a smooth large scale component and a rough small-scale turbulent component. The latter is specified as a random field uncorrelated in time. Subsequently, the material derivative is modified and leads to a stochastic version of the material derivative to include a drift correction, an inhomogeneous and anisotropic diffusion, and a multiplicative noise. As derived, this stochastic transport exhibits a remarkable energy conservation property for any realizations. As demonstrated, this pivotal operator further provides elegant means to derive stochastic formulations of classical representations of geophysical flow dynamics.