Unless Boro can reproduce their away form at the Riverside Stadium, they are set to slip out of the promotion race.
Manager Gareth Southgate must find a solution to the contrasting fortunes of his team or he will come under increasing fire from disgruntled fans.
Tom Cleverley, on loan from Manchester United, continued his good scoring form with his fifth goal of the season.
The goal in the 20th minute was set up by Danny Graham, a project of Middlesbrough's highly successful Academy some years ago.
Graham was released because his first-team opportunities were restricted through the presence of established stars.
Middlesbrough were the more enterprising side in the early stages with Adam Johnson their most skilful forward.
Johnson has been linked with a number of top clubs, including Real Madrid and Chelsea, so there is already speculation over whether Middlesbrough can hold on to him in the January transfer window.
Watford shook the 18,000 crowd when they took the lead in the 20th minute. Cleverley gave goalkeeper Brad Jones no chance with his shot from 18 yards.
Middlesbrough hit back but Mark Yeates fired well off target and then Gary O'Neil sent a fierce drive over the bar.
Watford's Lloyd Doyley was booked for a foul after 37 minutes though he pleaded to the referee that he had won the ball.
A Yeates cross from the left wing went right across the Watford goalmouth without a colleague providing the finish.
Watford goal keeper Scott Loach touched a Leroy Lita header round a post as Middlesbrough fought desperately for an equaliser before half-time.
Loach also brought off a fine save just after the break from Didier Digard.
Shortly after, Sean St Ledger headed into the Watford net but the jubilation of the 18,000 crowd was cut short when the goal was disallowed for a push.
Tony McMahon hit the underside of the Watford bar with a terrific 30-yard shot then his head in his hands as the ball bounced down to safety.
Watford battled hard and Middlesbrough struggled to achieve a breakthrough despite piling on pressure.
Manager Malky Mackay would have been pleased with the covering of his defence and the fighting spirit, but Watford looked an ordinary side.