Carlisle was told he could leave by Kevin Blackwell after slipping down the Elland Road pecking order and Watford boss Adrian Boothroyd wasted no time in signing him up.
Boothroyd, a former Leeds coach, told the Hornet's website: "He is exactly the type of defender I wanted."Clarke joined Leeds on a free transfer from QPR last season and made 38 appearances.
The former Blackpool trainee has initially joined on loan, allowing him to make his debut in tomorrow's opening fixture at home to Preston, and will make the move permanent on Monday.