Like Town's play-off defeat at Meadow Park in 2020, The Shaymen took the lead but were unable to maintain it.
But, unlike last year, Halifax battled back and salvaged something in a hard-fought clash that saw Wood cancel out an own goal with efforts from Josh Rees and ex-Shayman Scott Boden.
With Jay Benn and Jesse Debrah out injured, Town's defence picked itself as Pete Wild handed a debut to Javid Swaby-Neavin and retained Tyrell Warren.
Boreham Wood represented a significant test for Town after their formidable start, and the hosts started well, with Will Evans and then Femi Ilesanmi driving right through the heart of the visitors before their shots were blocked early on.
Boreham Wood had good movement and attacking intent, although The Shaymen didn't help themselves with some misplaced passes.
Somewhat against the run of play, a lovely move saw Waters played in down the left of the box and his low cross was turned into his own net by a Boreham Wood defender.
But the hosts responded with hunger and purpose, and just four minutes later, a shot by the impressive Frankie Raymond was turned in by the equally eye-catching Rees just inside the box, sending the ball the opposite way and leaving Sam Johnson with no chance.
Boreham Wood were aggressive and played with a real intensity, meaning Town could barely relax on the ball and had to try and match their hosts' drive and determination, making for a very watchable contest.
Play swung from one end to the other at times, such as when Boden squandered a big chance at one end when Johnson kept out his shot one-on-one, and then from Town's immediate counter-attack, Waters' shot was sent tamely wide from near the penalty spot.
The action again shifted from one box to the other as a nice one-two between Kieran Green and Jordan Slew preceded Green’s shot being blocked, prior to Kane Smith cutting inside and ballooning his shot wide.
But poor defending from a Boreham Wood corner saw Boden left with a free header in the middle of goal and the hosts' fightback was complete. And fight for it they had.
Rees should have made it 3-1 shortly before half-time but Town were again indebted to Johnson for keeping out his low shot one-on-one after Swaby-Neavin's loose pass had gifted the hosts possession.
Waters had again worked hard and offered a good outlet up-front for Town, but lacked support at times, with more needed from the likes of Harvey Gilmour and Jordan Slew to back-up his efforts. Behind them on the flanks, Swaby-Neavin and Warren struggled to offer much going forward in the way Benn and Jack Senior might have.
If Town were to get anything from the game, they'd certainly have to earn it. If a point looked a good result before the match, it looked even better by half-time.
Johnson was again tested when he parried Ilesanmi's shot from an angle a few minutes after the break.
But the game failed to reignite at the same pace or tempo after half-time, with any quality in the contest fast disappearing.
Town became the more dominant side as the second-half progressed, with the hosts getting deeper and The Shaymen wrestling superiority over the game. But turning that into chances proved difficult.
Waters hit the outside of the post from near the goal-line, but what had now become a disciplined, wily and well-constructed back five for Boreham Wood was problematic to penetrate.
Town's three changes had heralded more urgency in their play though, and after a decent spell of pressure, a corner found its way to Waters at the far post, and he lashed the ball home.
Halifax finished the game the better side, and the impressive Matty Warburton forced a save from Nathan Ashmore deep into added time, but a point was more than acceptable.
Boreham Wood: Ashmore, Smith, Ilesanmi, Evans, Fyfield, Mendy, Ricketts, Rees (Stephens 94), Raymond (Smith 78), Boden (Clifton 84), Marsh. Subs not used: Green, Munns.
Scorers: Rees (27), Boden (39)
Shots on target: 5
Shots off target: 6
Halifax: Johnson, Swaby-Neavin, Warren, Maher, Bradbury, Woods (Spence 75), Green, Slew (Allen 75), Warburton, Gilmour (Vale 70), Waters. Subs not used: Tear, McDonagh
Scorers: own goal (23), Waters (79)
Shots on target: 2
Shots off target: 7
Attendance: 503 (60 away)
Referee: Scott Tallis
Town man of the match: Sam Johnson, produced some strong saves to keep out some clear chances for the hosts.