There are a number of things that can go wrong with a water crossing. We've only had ours deep enough for water to wash over the bonnet, but it didn't quite reach the windscreen. There were no leaks or wet areas in the carpet, no stalling, no problems whatsoever. Keeping the following in mind will help with any water crossing:
1) Use a wading bra. Even without a snorkel, some water crossings can be done as long as you have a wading bra and keep the forward motion steady. The wading bra will also minimise the risk of debris entering the engine bay and damaging the intercooler/radiator/air conditioning.
2) If you're unsure about the river bottom, WALK IT FIRST. If it's flowing too fast for you to walk it, it is DEFINITELY flowing too fast for you to drive it. Find another way around.
3) NEVER enter the water when your turbocharger has been boosting heavily moments before. Despite the D40 having a water-cooled turbo, it can still get hot enough to do damage if it is dunked in water.
4) NEVER enter the water quickly - ALWAYS use 4LO and first gear. The radiator is restrictive to water flowing through it and a surge of water will push it back against the cooling fan, destroying one or both.
5) NEVER stop while in the water. Just keep moving. Even if you see the biggest fish in the world swimming towards you, just keep on going.