Hunt had gone 15 months without a goal after serious foot and knee injuries but made it three goals in three games early on to put the Royals ahead.
But Malky Mackay's side battled back to level before the interval when Troy Deeney was left free to head home and leave Brian McDermott's men again frustrated.
Reading are only two points off the play-off places but need to turn draws into wins if they are to challenge for a place in the Premier League.
Jobi McAnuff threatened against his former club with a mazy run before Hunt put the Royals ahead in the 15th minute.
Shane Long broke the offside trap to race clear down the left and had the presence of mind to pick out his Republic of Ireland compatriot in the middle for a low finish.
It was Hunt's third goal in as many games since returning from a long-standing injury and he gave England Under-21 goalkeeper Scott Loach no chance.
Simon Church almost broke clear as the visitors' pace up front looked a real threat but Deeney levelled against the run of play five minutes before half-time.
Jordon Mutch swung over a corner from the left and Deeney was left unmarked to power in a header.
Hunt smashed in a fine strike right on the stroke of half-time to force a good save from Loach but the England man got right behind it to hold on.
Ian Harte came off at the break and both sides struggled to find their feet in a scrappy opening 10 minutes.
Don Cowie put in a dangerous cross for Watford but could not find a team-mate before Long charged down a clearance and looked set to burst into the area only for Adrian Mariappa to make a fine saving challenge.
The dangerous Cowie shot wide as both sides looked for a third goal in the game but for all their endeavour there was a lack of cutting edge on display in the final third.
Reading introduced winger Jimmy Kebe on his return from a knee injury and he played a part as Church came close with a low shot at the end of a sharp attack.
Long was then denied by Loach and midfielder Jem Karacan put the rebound over the top to waste the best chance of the match.
Loach had been in top form to keep out the Royals but was fortunate late on not to concede a penalty when he appeared to barge into Long while claiming a cross.
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