In the episode 'whiterabbit' a girl is drowning in the sea. Charlie tells Jack abou the girl and also tells him he does't swim. But at the end of season 3 we see Charley swimming down to the underwater laboritory perfectly fine.

Editor's Note: Two things. 1. He might have had a reason to say that he couldn't swim. 2. There are people that cannot swim on top of the water nor rescue somebody but are perfectly fine swimming underwater. I know, because I am that way.