Paul Devlin, Danny Webber and Scott Fitzgerald scored as Watford extended their unbeaten run to six matches.
The result means Wimbledon are looking for their first win at the National Hockey Stadium and leaves the team anchored to the bottom of the Division One table.
The match, designated all-ticket, was played in front of a poor crowd of 6,115 despite the presence of 2,000 away supporters, with the home team forced to turn away fans who wanted to pay on the day.
And the Dons afternoon got off to a terrible start when striker Patrick Agyemang limped off with a knee injury in the eighth
Hornets winger Devlin then put Watford ahead with a right-foot volley on 22
minutes after Paul Heald had saved Webber's initial effort.
And things got worse for the home side when Peter Hawkins was stretchered off.
Webber converted Devlin's touchline pull-back to double the Hornets lead after 33 minutes.
Wimbledon forced their way back into the contest four minutes after half-time when Mikele Leigertwood rose unchallenged to head home a Wade Small free-kick from eight yards.
But Fitzgerald restored the two-goal cushion with his sixth goal in seven
starts on 67 minutes.
Dons defender Nico Herzig headed a Watford corner back against his own
crossbar, where Fitzgerald was lurking for the easiest of tap-ins - and moments later Webber struck the upright from Devlin's cross.
But despite their woeful defensive performance Wimbledon continued to press forward and Jobi McAnuff was denied by a goalline
clearance from Hand.
But Watford were showing no mercy, and Fitzgerald could have made it four with a late header that he put just wide.
Wimbledon: Heald, Kamara, Leigertwood, Herzig, Hawkins,
McAnuff, Chorley, Reo-Coker, Small, Holdsworth, Agyemang. Subs:
Nowland, Gray, Tapp, Darlington, Worgan.
Watford: Pidgeley, Kelly, Cox, Gayle, Smith, Hand, Ardley,
Vernazza, Devlin, Webber, Fitzgerald. Subs: Chamberlain, Dyche,
Dyer, Brown, Cook.
Referee: L Mason (Lancashire).