Bolton continued to dominate the early stages and Keith Andrews twice fired over the bar with 15 minutes on the clock.
It might have been 2-0 late in the half when Marcos Alonso struck from distance, but his effort moved wide of the post.
There was time for one final chance, and Kevin Davies made it 2-0 to the home side with a cool finish moments before the break.
Bolton continued to dominate the early stages of the second period, and Davies came close to adding his third with 53 minutes on the clock.
Watford were back in the match just before the hour mark, however, when Lloyd Doyley hit a curling strike into the top corner.
Mark Davies came close to adding a third for the home side late on, but it remained 2-1 with Bolton securing three much-needed points.