Malky Mackay's men doubled their advantage before half-time when fellow loanee Martin Taylor snuck in behind Lewin Nyatanga to find the back of the net.
City boss Gary Johnson made four changes from the side that drew 1-1 with Coventry at the weekend with Lee Johnson, Cole Skuse, Alvaro Saborio and David Clarkson replacing Paul Hartley, Marvin Elliott, Evander Sno and top scorer Nicky Maynard.
Opposite number Mackay made just one change to the Hornets line-up after their defeat by Barnsley as Danny Graham came in for Ross Jenkins in an attacking role.
The home side started brightly and should have taken a second-minute lead when a Don Cowie inswinging corner found the unmarked Martin Taylor who headed just wide, before Henri Lansbury found Cowie who headed wide.
City tried to fight back the early onslaught when Clarkson found himself in acres of space to find Lewin Nyatanga who headed just wide of the post.
But it was Watford who took the lead in the 14th minute when Mariappa danced his way beyond Saborio to cross for on-loan Helguson to peel off his man to power a downward header beyond Dean Gerken.
Saborio should have made amends just three minutes later when he headed wide from a Bradley Orr pin-point cross, before Cole Skuse drilled an advantageous 35-yard shot narrowly over the bar.
The Hornets doubled their advantage in the 34th minute when Saborio fouled Jay DeMerit just outside the area, Lansbury's quickly-taken free-kick found Taylor, who managed to outmuscle the towering Nyatanga, to superbly volley home his first goal since joining on loan from Birmingham.
Helguson should have grabbed his second when he latched on to the end of a Graham cross-field ball only for him to head inches over the bar.
Robins boss Johnson made two changes at the break when Saborio replaced Marvin Elliott and Jamie McAllister replaced Ivan Sproule.
City thought they had grabbed a goal back five minutes into the second half when Liam Fontaine brought a fantastic save from Scott Loach who superbly parried the defender's header to safety.
Openings were few and far between after the break for both sides with Orr and Sproule seeing tame efforts collected by Loach.
Watford could have extended their lead in the 75th minute when substitute Liam Henderson's thunderous strike was well defended to safety by Nyatanga.
Mackay's side continued to push for a third goal with Henderson again seeing an effort go narrowly wide late on.