I have plenty of sand that collects somehow between the doors and the seals from just driving around in the winter on sand/salt covered roads.
I also had some water seep in through the rear hatch, around the tail light and under the carpet everytime it rained. This water would then stick around the cargo area, and make it's way downhill under the rear passenger seats and down to under the carpet of the front seats. It would smell like wet dog everytime the heater was on blowing on the floor.
You can check if there is water in you trunk under the carpet pretty easy. I think it was only held down by the plastic covering at the end, and just slid under the side panels. Also you can pull the little cover in the trunk where the jack is stored and look down to see if there is moisture, and you can remove the access panels to change your tail lights and look down to see if there is moisture.
Unfortunately, stuck on behind the carpet it some thick cloth/cotten/lint not sure what it is insulation. It soaks up all the water, and keeps it. I removed all my interior, and removed the carpet, and left it outside to dry for days, but it never dried and always smelled.
Eventually I took the time to remove that backing in whole chunks and traced them out on my own insulation material. I washed the carpet, and put back my own insulation material.
No amount of carpet cleaning fixed the smell because it wasn't on the carpet, but under the carpet.