How do I get the Nightingale out of the water?

Before leaving the sanctuary, be sure to talk to Karliah or both she and Brynjolf may become stuck underwater. At this point you will not be able to talk to her, essentially breaking the quest.

• Use the console commands prid 58F1A and then moveto player. This way you can talk to her and continue the quest.
• Alternatively, you can 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 (if you are not playing as an Argonian).
• Another option is to shoot her with arrows when she is in sight from the land. She will run up at you. If you have a potion of paralysis, paralyze her when she is on land. Exit and come back.

Source: UESP