When I need to really clean carpet (in the car or in the house), I fill up a pump sprayer with assorted cleaning products (including dish soap, oxyclean, simple green degreaser, odoban disinfectant, carpet stain remover) and mostly water. Test your mixture under the seats first to make sure it doesn't change the color of the carpet. Soak the area down good, and suck it up with a wet/dry vac. Let the car air out, as you just introduced a lot of liquid to the car, and want it to all evaporate away ASAP.
If this does not work, you will need to remove the carpet to determine the extent of the damage. The mold may be in the insulation. It is also possible the water will pool under the back seats. Don't forget the trunk, this is a popular place for leaks.