Nicolas Anelka was the hero for the Trotters, scoring the only goal of a wretched game on 62 minutes by firing through a crowd of players from 12 yards.
Anelka had been a doubt before the game with an ankle injury but he gave Sam Allardyce a boost by declaring himself fit. The Bolton boss replaced Ricardo Gardner with Tai Ben Haim in the only other change from the side who drew with Charlton in midweek.
Watford manager Aidy Boothroyd rang the changes following the mauling at Old Trafford in midweek. England keeper Ben Foster replaced Richard Lee in goal, Malky Mackay returned to the heart of defence, captain Gavin Mahon was passed fit after missing the last three games with a calf injury, while Lee Williamson was handed his debut on the right-hand side of midfield.
Anelka enjoyed the first shot on goal, following a 20-yard free-kick over the crossbar, but the next goalmouth incident of a scrappy opening did not arrive until the 20th minute. Williamson won a free-kick down the left and his centre was just headed over at the far post by Jay DeMerit, who did well to get past Abdoulaye Meite.
A minute later Jordan Stewart saw a goalbound shot from a short corner routine flick off the head of Gary Speed and fly over the visitors' crossbar. Mahon was the next player to try his luck, sending Jussi Jaaskelainen scrambling across his goal with a left-footed shot that went just wide.
Bolton struggled to get any fluidity into their attacking play in a stop-start game but they threatened twice in the space of a minute just before half-time. Anelka forced a flying save from Foster with a left-foot blockbuster, while Speed sent a glancing header from El Hadji Diouf's cross just past the far post.
Boothroyd made one change at the break, replacing Williamson with another debutant Gareth Williams, in a bid to help his side retain possession. And the manager would have been delighted to see his side start the second half on the front foot. In one early attack from neat interplay between Mahon and Mackay sent Adrian Mariappa haring down the right after his cross flashed across the face of goal.
At the other end, Andranik Teimourian, on as a substitute for the injured Stelios Giannakopoulos, saw a right-footed drive tipped around the post by Foster on 57 minutes.
Foster though was at fault for the only goal of the game just past the hour. His unconvincing punch from a Speed corner fell straight at the feet of Anelka who took one touch before firing low through a crowd of players for his eighth goal of the season.
Watford went for broke in the final quarter of the match, fielding three players up front, including new signing Steve Kabba, but they failed to breach a well-organised Bolton defence and drew a blank for the 13th time this season.