Usually, its the plastic water barrier between the door panel and the door. People do not realize that they actually serve a function. When it rains, the water enters between the window scraper and the glass. It sheets down and exits between the door panel and the door. It then collects on your floor.
Pull the door panel and make sure the plastic barrier is there. If not, go to your hardware store and buy some double-sided carpet tape and some heavy mil plastic. Install the double-sided tape where the original glue was. Then, install the plastic. Cut out the holes for the door clips, window crank, mirror remote and armrest holes with a sheetrock knife. Install your door panel and hardware. Problem solved.
While I'm in there, I usually clean out any debris along the bottom edge of the door to prevent rusting. I do this by breaking up the dirt/dust with a thin screwdriver, and then vacuuming it all out with a shop vac. I also take the time to completely remove the window regulator and grease the hell out of it with some white lithium grease. They tend to bind up without lubrication.
An alternate possibility for water getting into your truck: at one time, my truck had a tonneau cover. Someone drilled holes into the cab for the mounting hardware. Whenever it rained, water would wick into the holes and pool on the bottom under the seats.
Lastly, check the rear window seal.
Having said all that, it's probably the water barrier.