Another borrowed striker, Lukas Jutkiewicz, put Wanderers in the lead before Mason, made his second debut for the Trotters this season, gave them breathing space just before half-time.
The Hornets then did not look threatening as their five-game unbeaten run came to an end.
Wanderers carved out the first opportunity of the game.
Mark Davies burst through the visitors defence before playing through Mason one-on-one with Manuel Almunia.
However, Mason's shot at goal was tame, giving the former Arsenal stopper the chance to save the ball with his feet.
It was then Watford's turn to almost take the lead.
Ikechi Anya went wide before cutting back a cross to the head of Troy Deeney on the edge of the six-yard box.
But, despite having power in the header, Adam Bogdan produced a superb save from point-blank range to deny the Hornets.
With the visitors deep in the Trotters half, Alex Baptiste then punted the ball upfield, finding Mason on the break in the process and again through on goal.
This time, the forward rounded Almunia, but his touch just gave the defence time to recover and send the ball out for a corner.
The resulting corner then saw Mason connect perfectly with Davies' cross, though Almunia was perfectly positioned to catch the powerful effort.
However, it was not long after that the home side had the ball in the net.
Jutkiewicz converted his second attempt from Medo's cross, only for the referee to pull the game back for a foul on the provider.
That did not make much difference, as from Jay Spearing's resulting set-piece, Jutkiewicz was on hand to tap the ball in and score at the back post.
They then doubled their advantage on the stroke of half-time and it was a case of third time lucky for Mason.
Neil Danns won a header which put the former Plymouth forward through on goal again. This time he made no mistake, showing composure when placing the ball past Almunia.
Bolton continued to play on the front foot through the second half and they could have easily extended their advantage.
Medo had his free-kick from range fizz just wide of the top corner before Danns had his acrobatic effort saved by Almunia.
Sean Murray then had the chance to hit-back for the visitors, but he could only direct his half-volley inside the box straight down Bogdan's throat.
Mason really should have got his second of the game after he was put through again by Danns, though Almunia once again managed to get the better of the Irishman before the game petered out.