I have used my R80GS to cross some rivers in Iceland and Africa and have found that you can go until the waters gets into the airfilter. But you might get some “small” problems before it happens:

-If you spend a long time thinking (or taking a break) in the middle of the river the clutch-housing will be full of water, and the clutch will start to spin, normally you can continue driving. When you get out of the river the water will come out everywhere – quite amusing and a great photo-opportunity!
This might be solved if you cover the holes in the starter-cover, I think most of the water enter here but it’s not a big problem.

-If you go fast downhill into the lake the “splash” from the water might fill the airbox and the engine stops. Depending on the water-temperature your feet will get very cold when you drain the filter-housing (there is a rubberthing you can remove to drain it).
An easy way to avoid this is to cut the bottom out of two plastic-bottles and cover the air-intake but it is even better to rebuild the stupid snorkels…

I have not had any problems because my carbs or plugs has been under.

If you plan to use the GS for a submarine for a long time it is smart to attach a tube to the ventilation in the cardan and gearbox so it doesn’t suck a lot of water. I haven’t done this and it’s quite impressing how much water you can have in the oil before anything breaks…

If you stop the engine there is no limits…. Cover the airbox, exhaust and maybe the vent in the gearbox and cardan and start to walk…. Hmm, might be an option to remove luggage.

Diving GS: http://www.actiontouring.com/offtheroad.html

Happy swimming!