We consider the motion of a particle governed by a weakly random Hamiltonian flow. We identify temporal and spatial scales on which the particle trajectory converges to a spatial Brownian motion. The main technical issue in the proof is to obtain error estimates for the convergence of the solution of the stochastic acceleration problem to a momentum diffusion. We also apply our results to the system of random geometric acoustics equations and show that the energy density of the acoustic waves undergoes a spatial diffusion.