Forward Junior Morias successfully came through a work out on Tuesday afternoon as the Cobblers welcomed a young Watford team to the PTS Academy Stadium.
Northampton Town had the opening opportunity when Waters was clipped outside the box. Dean Bowditch struck a decent effort from the free-kick but the ball whistled over the bar.
The Cobblers broke the deadlock in the 10th minute with Morias playing a big part in the goal. Waters was released in to the penalty area and drilled a low cross towards the 6 yard box where Morias saw his effort saved, only for the ball to fall to Dean Bowditch to tap-in on the line.
Morias was in again on 16 minutes, his burst in-behind the Watford defence was spotted by Jordan Turnbull who played an impressive diagonal pass to pick the forward out, but his first-time volley was saved.
The visitors then ventured forward on 18 minutes and after some neat play the ball was worked to the edge of the box for a strike to come in, but keeper Lewis Ward was there to make a decent save and Leon Barnett was in quickly to clear the danger.
The advantage was doubled on 22 minutes through Kevin van Veen. Sean Whaler and Bowditch combined well on the left before Bowditch picked out van Veen's well-timed run into the box and the Dutchman kept his cool to find the net from close range.
The ball in-behind was proving a successful tactic with Morias always a willing runner. He came close to adding to the tally on 30 minutes after being played through but the Watford 'keeper made an impressive save to turn the ball behind for a corner.
Midfielder Morgan Roberts and under 18's goalkeeper Bradley Lashley were introduced at half-time with the Cobblers continuing to dominate the majority of possession from the restart.
Camron McWilliams was a constant outlet moving forward from right-back and he earned a free-kick on 55 minutes. van Veen struck the free-kick from 30 yards but it was comfortable for the Watford 'keeper. McWilliams then recovered brilliantly at the other end to block a shot on the edge of the box after Watford broke forward on 58 minutes.
The next chance of note was on 65 minutes. Waters again had space in the box to drill in a low cross which the 'keeper initially palmed back into the danger area and Roberts was there to meet the ball but was denied by a last-ditch block.
Waters' hard work then paid off as he got himself on the scoresheet moments later. A well timed run saw him get in-behind the Watford defence and his first-time lobbed finish from the edge of the box found the back of the net to make it 3-0.
Both sides then made a few more changes and it was the visitors who had the next chance. After some good possession in midfield the ball was worked back to the young Watford captain but Lashley was alert to dive low and save his cross/shot.
The visitors were then awarded a penalty on 80 minutes which was well dispatched by Watford's number 7 to reduce the deficit to 3-1. Lashley was then called into action to deny Watford another 3 minutes from time, getting down low to deny a strike from just inside the box.
The Cobblers nearly added a fourth on 89 minutes. A corner from the right fell for Roberts 12 yards out but his goal-bound effort was deflected against the post by the defender on the line.
Under 18's midfielder Michael Harding then showed neat skill to create space in the box but fired into the side netting in the game's final chance as the Cobblers saw out the 3-1 win.