
Former Burnley forward Andre Gray opened the scoring in the third minute with a superbly-taken volley from a fine Deeney cross from the right flank.
Three minutes later, though, Burnley got back on level terms when James Tarkowski rose well at the back post to head in a Jóhann Berg Guðmundsson corner.
After an evenly-balanced and entertaining first half, Watford hit Burnley, who have now gone seven league games without a win, twice after the break.
Deeney drove home in the 48th minute after being found in the box by Abdoulaye Doucouré. Then, a terrible giveaway by Burnley defender Matt Lowton to Hughes resulted in the Watford midfielder firing past Joe Hart with a brilliant left-footed strike.