You might recall that there was a pool/entry into the station from underneath that was open to the ocean which people could use to swim up and into the station. The only thing that keep that pool "level" and prevented it from filling up the station with water was the air trapped in station.
getting overtly nerdy and nitpicky, there's no way the station that large would fill with water because of a window-sized hole. the physics wouldn't allow the air to leave quick-enough to force the pool water to rise.
That's not my explanation. That's the explanation I recall was bandied about at the time as to why he locked himself in there.
In addition, I think a valid argument can be made that Charlie "wanted" to die. He had cheated death many times (if you believe Dexter's premonitions) and the more he did so the more he was convinced that had eventually had to die to save Claire and the kid. Therefore, even if Charlie could have found a way out in time, I don't think he wanted to.
now that, i'll take as a valid theory.
Same thing. As much as I'd like to take credit for it, that was something persons in authority over the show said back when that episode aired. I think it's pretty much, along with the nerdy and nit-picky stuff above, the "official" motivation.
