But Vydra equalised when he coolly stroked the ball home from 10 yards.
And Almen Abdi earned victory when he shot into the bottom corner.
Bolton, who slip to just two places and three points above the relegation zone, had started brightly enough and looked well set for at least a point when Sordell calmly found the bottom corner of the net from the spot.
But Watford had created the better chances up until then, notably when Troy Deeney was denied by the legs of away keeper Adam Bogdan.
On-loan Udinese striker Vydra
showed great footwork and composure to run through Bolton's defence and level before the break after Cristian Battocchio had flicked the ball forward.
The hosts, top scorers in the Championship this season, chased a second goal and continued to have the upper hand in a scrappy second half.
Eventually the pressure told as Abdi gave them the lead from the edge of the area after a sustained spell of possession.
The Hornets dominated the closing stages and easily held on for victory.
Full Time The game is over, as the referee blows his whistle.
Nyron Nosworthy restarts play with the free kick.
90:00 +4:04 Substitution
Substitution John Eustace joins the action as a substitute, replacing Cristian Battocchio.
90:00 +4:04 Booking
Booking Steve De Ridder is cautioned.
Steve De Ridder gives away a free kick for an unfair challenge on Daniel Pudil.
Almen Abdi takes a shot from just inside the penalty box which clears the crossbar.
Short corner taken by Matej Vydra from the right by-line.
Matej Vydra takes a short corner.
Corner taken short by Matej Vydra.
The ball is swung over by Zat Knight, save by Manuel Almunia.
Nyron Nosworthy takes the direct free kick.
Booking Samuel Ricketts goes into the book for unsporting behaviour.
Free kick awarded for an unfair challenge on Cristian Battocchio by Samuel Ricketts.
Free kick awarded for an unfair challenge on Almen Abdi by Jay Spearing. Free kick taken by Fitz Hall. Matej Vydra gives away a free kick for an unfair challenge on Zat Knight. Adam Bogdan restarts play with the free kick.
Nyron Nosworthy challenges Kevin Davies unfairly and gives away a free kick. Jay Spearing takes the direct free kick.
Substitution Nathaniel Chalobah leaves the field to be replaced by Jonathan Hogg.
Lloyd Doyley gives away a free kick for an unfair challenge on Chung-Yong Lee. Strike on goal comes in from Marcos Alonso from the free kick.
The ball is swung over by Zat Knight, Manuel Almunia makes a save.
Cristian Battocchio gives away a free kick for an unfair challenge on Steve De Ridder. Jay Spearing takes the direct free kick.
Substitution Nyron Nosworthy joins the action as a substitute, replacing Joel Ekstrand.
Daniel Pudil takes the free kick.
Substitution Marvin Sordell leaves the field to be replaced by Kevin Davies.
Substitution Joshua Vela leaves the field to be replaced by Craig Davies.
Substitution Steve De Ridder on for Chris Eagles.
Booking Jay Spearing goes into the referee's book for unsporting behaviour.
Free kick awarded for an unfair challenge on Matej Vydra by Jay Spearing.
Unfair challenge on Cristian Battocchio by Jay Spearing results in a free kick. Free kick taken by Cristian Battocchio.
Booking Almen Abdi is cautioned by the ref for unsporting behaviour.
Assist on the goal came from Matej Vydra.
69:29 Goal scored
Goal! - Almen Abdi - Watford 2 - 1 Bolton Almen Abdi fires in a goal from just inside the area to the bottom right corner of the goal. Watford 2-1 Bolton.
Darren Pratley takes a shot. Daniel Pudil gets a block in. Corner taken by Jay Spearing, clearance made by Daniel Pudil.
Booking Marco Cassetti receives a caution for unsporting behaviour.
Booking Darren Pratley is shown a yellow card for unsporting behaviour.
Corner taken by Jay Spearing from the right by-line, Troy Deeney manages to make a clearance.
Marco Cassetti concedes a free kick for a foul on Darren Pratley. Direct free kick taken by Jay Spearing.
Inswinging corner taken by Jay Spearing from the right by-line, Troy Deeney makes a clearance.
The ball is delivered by Samuel Ricketts.
Foul by Marco Cassetti on Marcos Alonso, free kick awarded. Marcos Alonso restarts play with the free kick.
Corner taken right-footed by Jay Spearing, Troy Deeney makes a clearance.
Joel Ekstrand produces a right-footed shot from just outside the penalty box that misses to the left of the target.
Shot by Marvin Sordell from deep inside the penalty area misses wide to the left of the target.
Daniel Pudil delivers the ball,
Outswinging corner taken from the right by-line by Almen Abdi, Zat Knight manages to make a clearance.
The ball is swung over by Marco Cassetti, Tim Ream makes a clearance.
Inswinging corner taken by Almen Abdi from the left by-line played to the near post, Jay Spearing makes a clearance.
The ball is delivered by Lloyd Doyley, Zat Knight manages to make a clearance.
Marco Cassetti gives away a free kick for an unfair challenge on Marcos Alonso. Marcos Alonso takes the free kick.
Free kick awarded for a foul by Matej Vydra on Darren Pratley. Samuel Ricketts restarts play with the free kick.
Daniel Pudil produces a right-footed shot from the edge of the box and misses to the right of the target. Corner taken by Almen Abdi from the right by-line to the near post, clearance made by Marcos Alonso.
The ball is crossed by Daniel Pudil, Tim Ream makes a clearance.
Jay Spearing takes a shot. Save by Manuel Almunia.
The ball is sent over by Darren Pratley, Almen Abdi makes a clearance.
The referee blows his whistle to start the second half.
45:00 +1:14 Half time
Half Time The half-time whistle blows.
Shot from outside the penalty box by Troy Deeney goes wide right of the goal. Outswinging corner taken right-footed by Almen Abdi, Fitz Hall produces a right-footed shot from inside the area that clears the crossbar.
Centre by Cristian Battocchio, save made by Adam Bogdan.
The offside flag is raised against Marco Cassetti. Adam Bogdan restarts play with the free kick.
The assist for the goal came from Almen Abdi.
35:17 Goal scored
Goal! - Matej Vydra - Watford 1 - 1 Bolton Matej Vydra scores a goal from inside the penalty area to the bottom right corner of the goal. Watford 1-1 Bolton.
Marco Cassetti crosses the ball, Joshua Vela manages to make a clearance.
Free kick awarded for a foul by Fitz Hall on Marvin Sordell. Chris Eagles produces a shot on goal direct from the free kick, save by Manuel Almunia.
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