If you have your waves (water shader or PF) pull it through a warp shader. As warper, you use a vector displacement shader, and as function input of that you use a get frame number (no input needed). If you set certain values (needs experimentation) in the vdisp shader, each frame will change the waves. You have to take into account the number of frames in a second and the amount of meters you need to shift waves in respectively X, Y, Z, so some calculation is needed.