I made a test of one way to do it.
http://www.youtube.com/watch?v=M5a2rihMmMo1) Create a scene with just the water that you want. Place the camera to where the entire view is taken up by the water (looking at a fairly steep angle). Export a video of the water.
2) In the scene where you want rising water, place a plane from the "3D Space" props. In the diffuse channel of that plane, change it to the water video. Now you have a plane of water that you can raise/lower.
3) Play with the rotation of the plane so that the water flows in the right directly. Adjust the opacity and reflection. In my video I also increased the scale of the plane so the waves would appear to be getting larger.
It gets the point across, but you can probably make it look better with some particle effects of splashes, if the water is rising quickly.
- Keith