Watt and Englishman, Neil Raymond, finished at 6 under for the 36 holes played on both the Country Club Brookline and Charles River Country Club layouts in Massachusetts. They finished three shots clear of a group of players who shared third position.
Watt, currently Australia's leading male amateur, birdied his final hole of the round to join England's Neil Raymond in the lead.
Watt's fellow West Australian, Oliver Goss, also did well, a round of 67 moving him from 19th to a share of 3rd position as he pursues an even better finish than his meritorious quarter final finish last year.
Victorian, Nathan Holman, also played the Charles River layout, one of two being used in the qualifying phase, recording a round of 68 to move from a share of 58th to 17th.
It was not such a good day for the remaining Australasians in the field. Taylor Macdonald, Daniel Hoeve, Brett Drewitt, Will Flitcroft and New Zealander Vaughan McCall finishing well short of the cut mark which fell at 4 over.
The opening round of the match play phase to determine the 2013 US Amateur Champion begins tomorrow.
Want video tips delivered straight to your inbox? Subscribe to iseekgolf.com newsletters.