Trougtyr,
If you want to replace your carpet after you stop the incoming water source you could order carpet from somewhere like this for example:
http://www.stockinteriors.com/AutoCa...FQKKaQodSUgDyA
The carpet installation is not difficult.
Loosen and remove the seat hardware, fold the seats to the right angle to get out of the door. Roll down your windows (so you don't scratch) and place a towel hanging over the door panels so you don't scratch them, open the doors all the way, and remove the seats one at a time. Pop the back seat up, and I think the trim on the sides just pops off too. Then kinda work the carpet out of the places it goes under around the edges that you don't want to remove because its a pain.
then if you are so inclined, when you have the carpet out, an inspection and cleaning should be done to ensure dryness, perhaps a wipedown and spray with wd-40 of potential problematic areas in the the floorboard area such as wiring harnesses and connector assemblies. You may even find you don't have to do this.
You might also remove ares of rust while you are there as a preventative measure by sanding, priming, and painting anything that looks like it could become a problem and might stain new carpet with rust stains (such as seat mounting hardware). Or if you're set on quickness, spray it all with rust converter and then some black spraypaint and call it.
You'll want to inspect any affected connectors such as powered seats etc, and clean them. For the most part I will assume the water did not become too terribly deep. If you have time, give it a day to dry/bake in the sun, just don't let it rain while its all open!
Then just reverse the operation, try going in with the carpet from the rear doors kinda installing it by hopping it in place towards the front. Depending on the mfg, you may have to trim a half inch here or there, but probably not. push the carpet under any trim you didn't remove and snap all trim back in place, reverse the seat procedure, (remember the towels on the doors so you don't scratch, and CAREFUL OF THAT PILLAR!), pop the back seat back down by squishing it like you have to do, and you're set!
It's really just like a big floormat!
If it turns out it isn't your trunk's fault,
Once, I had a problem with small leaves and debris getting into the plenum for the cars ventilation system, causing it to be unable to drain when it rains, and it would flood the entire car when it rains because of this; even though all seals were good. I had to change the filter and vacuum out the ducting and it stopped flooding the car. That seriously might be whats up. The filter is somewhat intended to not be changeable but with some handiwork you can change it out.
Hope I helped. If I missed anything, its been a minute since I've had the carpet up in the car.
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