The home side rarely had a kick in the first 25 minutes as Plymouth asked all the questions, hit the woodwork twice and opened the scoring in the 18th minute.
The Pilgrims could have been ahead after two minutes but Graham Coughlan saw his header hit the bar.
Eventually Plymouth's pressure finally told when David Norris broke down the right and crossed for Micky Evans to meet the ball with a crisp volley into the corner of the net.
Lee Hodges was unlucky when a fierce free-kick hit the inside of the post and came out across the line where it was scrambled clear.
It took 26 minutes for Watford to fashion a threatening attack and even this was halted for offside.
After 32 minutes with their first attempt, Watford equalised. Paul Devlin provided the cross and Neal Ardley was at the far post to head the ball past the keeper.
Watford keeper Richard Lee made a good save to block Paul Wotton's free-kick, but Plymouth may have been slightly lucky in the 44th minute when Luke McCormick manhandled Heidar Helguson as the striker broke away from him.
Manchester referee Eddie Evans issued a yellow and not a red card.
Watford took the lead in the first minute of the second half. Helgusson flicked on from a throw-in and Danny Webber broke, drawing the keeper before slotting home.
Then in the 58th minute, Watford cemented their lead with Ardley setting up Webber. McCormick came out in vain beyond his penalty area and Webber bypassed him before firing into the net.
Devlin and Helguson went close as Watford finished good value for the three points.