It's always going to just be an illusion, and it's a lot easier to pull off if the player never actually swims in the water.
There are a few key things you'll need to sell the effect:
1. Animated refraction material behind the glass. This will distort things, but not to the extent you would get from a regular water material (which won't render at the bottom or sides anyway).
2. Bubbles! Don't underestimate this trick - it can really, really sell the effect! Try Source2007's particle editor, or if you're not feeling adventurous enough, just use sprites.
3. Blue fog falloff. Above ground you fade to grey fog. Under water, it should fade to blue or brown, depending on how you want it to look.
4. Typical underwater props. Does this tunnel run along the sea floor Rapture-style? Add plant-life and rust!
5. Caustics. Not totally necessary and a bitch to pull off properly, but if you can get good looking caustics then your effect will be flawless.
6. Sound. Big, slow, booming metal groans & that flat reverb you only get when submerged in water.
7. Leaks. When all else fails, convince the player that they're genuinely under water by having some leaking into the tunnel. Even just a few drops leaking in at a seam in the tunnel could help sell it.
All these effects only work from the perspective of being in a dry tunnel running through the water. If the player has to swim at some point, you'll probably have to trigger them all to turn off and on when the player leaves and enters the tunnel respectively.