Having been separated following the play-off final defeat when Vydra joined West Bromwich Albion on loan from Udinese, the Czech international was reunited with Troy Deeney and both players scored in the first half.
Substitute Fernando Forestieri then made sure of the points with a third goal 10 minutes from the final whistle.
The Hornets were nearly gifted the ideal start to the season within 16 seconds when an awful back-pass from Dean Moxey let in Deeney towards the right side of the penalty area but he blasted his shot the wrong side of Andy Lonergan's near post.
Watford continued to make most of the early running and they opened their account in fine fashion in the 17th minute. Some confident one-touch play out of defence saw the ball worked to Gabriele Angella on the left flank and he advanced before lobbing a fine pass through to Deeney, who clipped it over the advancing Lonergan.
Having seen his strike partner of two seasons ago open his account, Vydra got in on the act himself six minutes later.
Released by an excellent long pass from Daniel Tozser, Vydra stayed onside as he raced clear to receive the ball in the right-hand channel before stepping inside Moxey's attempted challenge and drilling a low shot between Lonergan's legs.
Watford had other chances to increase their lead before half-time, while all Bolton had to show for their efforts was a Medo shot over the top.
Beppe Sannino's men nearly did add a third within 30 seconds of the restart when Juan Carlos Paredes, who impressed for Ecuador during the World Cup, thundered a right-footed shot against the crossbar from 25 yards with Lonergan beaten.
Jay Spearing saw a shot deflected behind but the hosts soon went close to scoring again as Vydra did very well to retain possession tight to the by-line before pulling the ball back to Abdi, whose shot was deflected agonisingly wide.
Moments later, a reverse pass from Lewis McGugan set Almen Abdi free in the penalty area but this time the Swiss midfielder was thwarted by Lonergan's legs.
Hornets keeper Heurelho Gomes was then troubled for the first time in the match, making a fine save to push behind half-time substitute Liam Feeney's well-struck 25-yard effort.
The former Tottenham Hotspur keeper was also forced into another good save in the 67th minute to tip over Chung-Yong Lee's well-struck dipping effort from 25 yards.
Substitute Jermaine Beckford fired into the side netting but it was another replacement, Forestieri, who made the points safe for the home side with ten minutes remaining.
The substitute had only been on the pitch a matter of 20 seconds after Vydra had made way when he latched on to a through ball following hesitancy in the Bolton defence and confidently rolled his finish between Lonergan's legs.
The visitors, though, refused to lie down and Lee forced a superb one-handed stop from Gomes with a close-range header before, from the resultant corner, substitute Dorian Dervite headed a clear opening over the top.