So I saw a couple people talk about underwater fortresses and I started to wonder would it be possible to make something rise or the water drain from something using red stone switches? I can't think of any mechanism that would let something rise or fall but I figure if you could find a way for water to flow through a open door then you could make something drain.
My first experiment was using water to get down to the bottom of my mine and use a red-stone circuit to cut off the water but the water didn't even flow through the open door
Nope! There are not currently any blocks that can either allow or not allow water based on their state. You can make sort of a once-off flood switch with TNT, but that's not exactly practical. Notch has said that he will be adding floodgates and stuff, so some day things like this will be workable.