There are rubber one way valves to drain water on the bottom of the door that are clogging. You have 2 choices, you can jam something up there like a pen, stick, etc to unjam the clog or you can do what I did when I got tired of the problem. That was just to grab the rubber valves with needle nose pliers and just yank them out and throw them in the trash. They get clogged with all sorts of dirt, leaves, etc that's in the rainwater and never really stay unclogged. Funny/peculiar sound when you're opening and closing the door and can hear water sloshing around though, huh?

By the way, there are a few of these all over the undercarriage of the car. Just get rid of them all.