Therea are a number of approaches to take with this (after the water leak is stopped. I have heard of this happening when a AC drainage gets clogged to when a seal in a window dries out). Actions you can take after the area is dry (use hair dryer if needed) include:
1)Try spraying it with some What Odor? It is a product you can buy in stores.
2) Buy a box of Pet Fresh at your local grocery/dept store. Sprinkle it all over your vehicle's carpet; let it sit for 10 minutes, then vacuum it up. Can also put a air freshener in your car.
3)Sprinkle baking powder on the carpet and/or seats where the water occured, rub into the upper part of your seats. After 24 hours vacuum the seats and carpeting.
If none of these three options work, a detail shop can help you with it. In most cases all three of these solutions will work for you. Good luck.