Uh... making lots of water, raising the terrain and then lowering it in game with triggers (not sure if this would work)
OR
Lower the terrain (or whatever you want it to do) and then add a water model with height or something to display the water in the desired lake. I suggest dummy unit so you can manipulate flying height.
disable watter height limits in the advanced menu, cover the area with watter, then flatten the terrain. use a terrain deformation to lower the ground in to a lake.
You can also use infrane's water model. I actually once made a system to flood the whole map gradually using that. Problem was, I couldn't have negative fly height, and when I moved the model down in an editor, WC3 had a nasty habit of deciding not to display the water when it should.