We present a numerical investigation of stochastic transport in ideal fluids. According to Holm (Proc Roy Soc, 2015) and Cotter et al. (2017), the principles of transformation theory and multi-time homogenisation, respectively, imply a physically meaningful, data-driven approach for decomposing the fluid transport velocity into its drift and stochastic parts, for a certain class of fluid flows. In the current paper, we develop new methodology to implement this velocity decomposition and then numerically integrate the resulting stochastic partial differential equation using a finite element discretisation for incompressible 2D Euler fluid flows. The new methodology tested here is found to be suitable for coarse graining in this case. Specifically, we perform uncertainty quantification tests of the velocity decomposition of Cotter et al. (2017), by comparing ensembles of coarse-grid realisations of solutions of the resulting stochastic partial differential equation with the "true solutions" of the deterministic fluid partial differential equation, computed on a refined grid. The time discretisation used for approximating the solution of the stochastic partial differential equation is shown to be consistent. We include comprehensive numerical tests that confirm the non-Gaussianity of the stream function, velocity and vorticity fields in the case of incompressible 2D Euler fluid flows.