Waterhouse pounced on a slip by Huddersfield full-back Scott Grix near the Giants tryline on 18 minutes for a simple score in the left corner before he polished off a slick move involving Richard Myler and Brett Hodgson on 24 minutes.
Hodgson, the veteran ex-Giants skipper, added the extras twice to help Warrington towards a comfortable 22-6 half-time lead. Mick Higham, Stefan Ratchford, Ryan Atkins and Hodgson also crossed the whitewash for Warrington.
Second-placed Huddersfield, who were looking to keep the pressure on Wigan at the top of overall standings, scored twice and started well as they grabbed an early lead.
Danny Brough's 40-20 kick on three minutes gave them the advantage with Craig Kopczak putting Jermaine McGillvary in for a converted try from the resulting scrum. The Giants were their own worst enemies, though, as they gifted Warrington their opening try four minutes later when Jason Chan knocked on.
Higham smuggled ball over the line through a crowd of players from the resulting Warrington play. Waterhouse's double came next, followed by another Giants blunder, a missed interception by the hapless Grix, that let in Ratchford for a simple score.
The game then boiled over on 38 minutes when Huddersfield centre Leroy Cudjoe was hauled into touch by three defenders as he went for a try. It sparked an ugly melee involving most players on the field, with referee Ben Thaler giving Chan and Warrington's Atkins lectures over their involvement.
There was simmering tension when Wolves were awarded a controversial penalty on the hooter, which saw Giants star Brough sin-binned for possible dissent. The needle between the two sides continued after the break, with Myler needing treatment after a heavy tackle. Home fans were incensed at the award of a penalty to Wolves.
Ratchford then helped put Warrington further ahead on 51 minutes with the pass for Hodgson to go over in the right corner. Teenage hooker Kruise Leeming then scored on his Huddersfield debut at the other end following an acrobatic off-load from Luke Robinson.
Any chance of a revival for the home side was snuffed out when Wolves scored their sixth try of the afternoon through Atkins on 68 minutes, with Hodgson converting to complete the scoring.
- Sports & Recreation
- Brett Hodgson
- Ryan Atkins
- Richard Myler
- Stefan Ratchford
- Scott Grix
- Mick Higham