I did not see any drain holes in the u-shaped channel that holds the weather stripping. I am not sure drain holes along the bottom of the channel would solve the problem. The weather stripping basically just snaps into the channel and moisture gets behind the rubber and has no where to go. At the same time there is no air circulation to help it dry. There are some rubber plugs on the bottom of the doors but these have nothing to do with the channel, I left them alone but avoided them with the bedliner.