Has been a problem, noted in other forum threads. There is an oblong rubber "plug" on the bottom of the (double-layer) floor pan on both sides. Take a screwdriver and you can carefully pry it out (use care to not tear the plug or bend the metal as you will want to replace this afterwards). Be prepared for water to come out (so have a pan handy or at the very least don't get soaked). Leave the plug out for a bit to dry, reinstall before driving. Somehow, the water gets in and then cannot drain out. However, resolve yourself of any thoughts of adding any drain holes in the plug or the floorpan - it will just cause worse issues. If you are concerned, talk to your dealer. 20" of water is pretty deep, actually; and right at the limit of what Jeep allows (but you already knew that, right?). If it was perhaps a little deeper or you were going faster than 5 mph, the wave action/water pressure could have allowed water to overtop and get into the area; and then could not drain out. 5 mph is pretty much a crawl or low range max speed. Best luck.
2011 GC Owner's Manual Page 372:
Driving Through Water
Although your vehicle is capable of driving through
water, there are a number of precautions that must be
considered before entering the water.
Your vehicle is capable of water fording in up to
20 inches (51 cm) of water, while crossing small rivers or
streams. To maintain optimal performance of your vehicle’s
heating and ventilation system it is recommended to
switch the system into recirculation mode during water
When driving through water, do not exceed 5 mph
(8 km/h). Always check water depth before entering,
as a precaution, and check all fluids afterward. Driving
through water may cause damage that may not be
covered by the new vehicle limited warranty.
Driving through water more than a few inches/
centimeters deep will require extra caution to ensure
safety and prevent damage to your vehicle. If you must
drive through water, try to determine the depth and the
bottom condition (and location of any obstacles) prior to
entering. Proceed with caution and maintain a steady
controlled speed less than 5 mph (8 km/h) in deep water
to minimize wave effects.