Making movin water is NOT easy
Ok, I made moving water in CTF-Aurinko]i[ and it was somewhat involved.
Rule #1 Do not make the entire level as a mover. Bots won't understand that and it would kill almost everything, including lighting.
Rule #2 Do not make zone portals out of movers. They do NOT work.
Rule #3 Use illusion instead.
The best bet is to use a combination of a mover and warp zone portals. Look at my map. There are two water locks with "moving" water level. Actually, the water stays just there where I put it, only the surrounding room moves.
To make the illusion, You have to isolate the player in such a way that (s)he can't see outside world while the water is "moving".
In my map I used an attach mover for the water lock room to keep the light box and the light travelling with it. Synchronization of the waterlock doors was another big issue.
This is a chllenging thing to do and when finished, You will get another challenge with the stubborn bots. You prolly end up putting bot-only kickers around the zone portals to slam them through those. They like to wobble around warp zone portals.
Good luck !