From the screens I'd say:
a) more entrances. That 1st screen shows how easy it would be to just camp in the corner and wait for someone to just hop up out of the water.
b) It's not really going to work because shooting in water is ridiculously slowwww and you have to have a certain amount of luck to be able to shoot/kill in water.
c) It doesn't really look like a bunker. I'm not sure what it looks like, there's just not a lot in it - it looks empty.
d) Don't use semi-opaque stone textures! use the plain white texturs with trans33 or trans66. I think 33 looks better - but it's been a while since i used bsp!
Keep it up, you've come a long way from myhouse.bsp
EDIT
oh, and, even if you can't be bothered, always light the map AS you make it, not after so that vising is just natural.