Linedef effect number 541, "Horizontal Wind", tag that to your water sector. Check the "Effect 4" box (By default it is effect 6).
The direction and length of the control linedef affect the strength and direction of the current. You could use "Horizontal Current" (544), but in this case they're identical. (Wind affects the entire sector, current affects the surface only on solid floors and on intangible ones anything inside it)