Do you want the type to look like it's in water, or to look like it is water? I'm not quite sure what you're saying.
If you're asking what I think you're asking, I have a couple of suggestions: Path text. Make some nice wavy paths and animate your text along it.
You would probably want to animate the text randomly off of its baseline using text animators.
There's actually a whole section of AE's help dedicated to animating text, you might want to look into it. Basically you want to use text animator or two.
There are also a large number of text animation presets! List here and a gallery of some of them here.
It wouldn't hurt to also check out this tutorial here on dropping a logo into some water (some of these techniques might come in handy for you.)