Several courtrooms on the third floor were closed all morning due to the cleanup; court appearances were shifted to alternate courtrooms. It was not immediately known when they would reopen.
Sheriff's department spokeswoman Eileen Hirst said the flooding problem began at about 7 p.m. Thursday.
Hirst said the last similar problem at the Hall of Justice happened in the 1990s, when flooding originating in the jails soaked several Police Department offices.
