This may help, it is from http://www.uesp.net/wiki/Skyrim:Blindsighted, bugs section.
Before leaving the sanctuary, be sure to talk to Karliah before exiting, as both Karliah and Brynjolf may become stuck underwater. At this point you will not be able to talk to her, essentially breaking the quest.
PC: Use the console commands prid 58F1A and then moveto player. This way you can talk to her and continue the quest.
PS3/xBox:Try swimming and bumping into Karliah repeatedly to knock her into the correct path and out of the water, at which point she will continue normally. This may take a while, so it is a good idea to have a waterbreathing enchanted item with you to prevent drowning. Although if you are playing as an Argonian this is not needed.
Edit: the other option is to reload your save from before the fight and replay it, then after the fight stay close to Karliah and try to speak to her before the water reaches the ceiling - I think it's if you leave it until the water is too high to enter dialogue (because her head is underwater!) that it glitches. I think!