Watford pulled further away from the drop zone while Wimbledon were sent closer to the relegation trapdoor.
Lee Cook started and finished a flowing Watford move for the opener which was aided by some poor Dons defending.
Watford's Lenny Pidgeley pulled off a fingertip save from Ben Chorley before Cook was fouled by Jermaine Darlington and Neil Cox scored from the spot.
Jack Smith's shot put Watford's 3-0 up and ex-Don Neal Ardley sealed the win when he converted Paul Devlin's cross.
Wimbledon could not be criticised for a lack of effort but they failed to find the quality to mount any real threat on the home goal.
They went behind when Cook broke forward and fed Scott Fitzgerald who in turn played a delightful through-ball to Devlin.
Devlin then laid the ball off to the advancing Cook and he made no mistake in slotting home beyond goalkeeper Steve Banks.
Cook was a constant thorn in Wimbledon's side and he earned the penalty for the Hornets' second before his pass found Jack Smith inside the box and the defender scored with a shot low down the centre of goal.
To their credit Murdoch's men continued to battle and Malvin Kamara struck the woodwork with a ferocious 35-yard strike.
But Ardley converted a Devlin cross with 76 minutes gone to help pull Watford further away from the relegation zone.
Watford: Pidgeley, Cox, Dyche, Ifil, Smith, Ardley, Hyde, Mahon, Fitzgerald, Cook, Devlin. Subs: Chamberlain, Vernazza, Dyer, Hand, Doyley.
Wimbledon: Banks, Darlington, Gier, Gordon, Hawkins, Barton, Campbell-Ryce, Chorley, Harding, Gray, Lewington. Subs: Jarrett, Mackie, Herzig, Kamara, Worgan.
Referee: R Olivier (W Midlands).