Seawater leak caused a reactor scram. Condensation in the high pressure air froze the air lines preventing an emergency blow. At least that was the best guess. Lots of procedures changed after that incident.
The loss of propulsion following the scram is what ultimately doomed the Thresher. Procedure at the time required a long process to restart the reactor, delaying restoration of propulsion. One of the first changes following the disaster was the implementation of a quick startup procedure, to get the screw turning again as rapidly as possible.
The water in the emergency blow lines resulted in the Sub-Safe system—strict controls on work on any ship’s system critical to the boats operation. IIRC, this was the genesis of the entire QA system in modern manufacturing.
I want to say that after we lost another boat that they redesigned procedures for designing and handling of torpedoes too.