I had a quick look through the attributes for the shader, but couldn't find anything that would animate it automatically.

For the water, I just followed the examples in the maya help files about creating ocean materials. It's a feature that's included in the unlimited version of maya - just a case of inserting an ocean plane, and then changing it's attriubutes to make it look foamy, still, stormy or to give a lava effect etc. Hope this helps, that's about all I did.