RupertMurdock: Ok, some kind of switches... do they operate a pump? I mean, can you see or hear one?
Not really. It just changes which areas are flooded. e.g. pulling switch X removes water from area A (thus giving you access to switches Y and Z), but might cause water to appear in area B.
It's not pumps. If I'm not mistaken, the switches open/close escape tunnel doors thus changing the water level.
Despite the way my original question is worded, it's fairly easy to solve this and get all the water out. You basically pull switches, which open new areas, then you try all switches in the new area, which open further areas (but as I said, might re-flood others) and so on. The difficulty lies in the water monsters, which might prove to be too much if your party is of not high enough level.
Another high level hint: it's not an obscure title, and it's avialable on GOG.