Think about it, if your window goes up and down, it's going to happen.
You would be better off taking the door panel off so you can understand the construction of your door.
I'd also check your window trim, if it's messed up, you will get an abnormal amount of water in there.
Every car on the market has a certain extent of this, it's inevitable, and it's why there's nothing of super importance in the doors. not to mention, another reason that we recomend car speakers and not home speakers or computer speakers.
Also, why is this in the fabrication forum?