I can be lazy sometimes and just want a quick run through the carwash, but the last couple times I have gone, I notice water running down along the passenger-side floor. It didn't happen the first few times I took my car through the wash, but now it's consistently happening.
And today as I was driving away, I took a right turn and water that had apparently stored itself for safekeeping in my battery compartment poured out the drivers side like a soapy flood. Upon popping the hood, I saw that the entire section was still wet (obviously).

What I'm wondering is if there should be a guard or trough of some sort to divert water from getting into the compartment? From the bottom of my windshield/wipers it goes straight down onto my battery... that just doesn't seem right!
Checking the forums, it says that the drains may be plugged, so I am also wondering if my local dealer would take care of that (free?) or if it's better off for me to try and do it myself?

 

There's a hole in the battery compartment area that is supposed to drain out the water that gets into there. Yours is most likely clogged. Pop the hood and take off the rubber lining and plastic cover for that area and start feeling around in between the batter and the ecu box. You might be able to see it. I can't really remember where exactly it is, but its a pretty easily found hole. Mine was clogged about a year ago during the rainy season here, frikkin sucked. Went out one day and had an inch of water on my floor boards. But just look/feel around in there and you should find it. It has a rubber grommet in it to keep you from slicing your finger. Also, there is another tiny one that the little rubber hose from the battery gets put into. In a pinch, you can pull that little hose out and the water will drain that way too. Just remember to put the hose back

 

^ What he said. There's probably a whole bunch of leafs that got stuck in there.

 

I tinkered around my battery compartment area, trying to find a way to clear the blockage, but I just couldn't get at anything. It is not easily accessible!

So I went to my mechanic (friend of the family), he raised my car and from underneath unblocked it using a very long screwdriver...

What came out was a LOT of stale water, and what looked to be some pieces of plastic that had completely blocked any flow of water.

All clear, now to wash my car properly...