I've been through the same type of ordeal. Brandon couldn't be more correct about the air intake.

A long story short, it was raining hard all day and lots of streets flooded. A friend driving his 1988 Oldsmobile Ciera came across a long puddle which actually turned out to be a mini lake a half a block long. The water was knee deep and without thinking, he plowed through. Water was splashing out from underneath the hood. We made it half way across and the car stalled (a kid standing on higher ground was laughing his head off at our predicament). Water was now seeping in through the door jams. After three minutes the car started and we made it out without it stalling again but the car died heading back to my house. We had it towed to my place and I had a look under the hood to give it a quick check. I found the air filter under water (the canister was completely filled). The following morning he try starting the car till the battery died. He had the car towed to his mechanic and got the car back 3 days later with a $1,000 in parts and labor. The engine blew the following year.
I also think you should have your car checked out.