"The dirt was unreal and all the riders were rapt. The Cardrona team and the Wanaka club did a sick job with the track."
Masters' only previous national downhill title was as a junior in Nelson over a decade ago.
"It has been a long time between drinks. But with the depth of the field out here today, I am pretty stocked to be able to wear the national jersey this year."
In a small field, Auckland's Kate Weatherly took out the elite women's grade in 3:27.93, ahead of Subway national performance hub rider Shania Rawson (Tauranga) in her first year out of the under-19 grade.
"The conditions were pretty much perfect and the track held up well. I wanted to go as hard as I could, have fun and not crash," said Weatherly. "Crankworx is the next big thing for me. I am still at university so can't do too many world cups but hoping I can do one or two depending on what I can fit in."
Masters will set his downhill bike aside now to compete in two Enduro World Series events in South America before heading to Europe in mid-April for the World Cup season.
"I've been working hard and building for a busy year ahead, so I am really stoked to tick this one off and hopefully keep the ball rolling."
MacDonald was second in the championship with Matt Walker third ahead of Keegan Wright and Wyn Masters.
Bay of Plenty's Tuhoto-Ariki Pene, who is a leading age-group BMX rider, took out the men's under-19 honours from Subway performance hub riders Josh Oxenham (Auckland) and Charlie Makea (Napier).
Results, Alterm New Zealand Mountain Bike Championships:
Male, elite: Ed Masters (New Plymouth) 2:51.09, 1; Brook MacDonald (Napier) 2:54.02, 2; Matt Walker (Kawerau) 2:55.50, 3; Keegan Wright (Rotorua) 2:56, 39, 4; Wyn Masters (New Plymouth) 2:58.00, 5.
Under-19: Tuhoto-Ariki Pene (Maketu) 2:59.09, 1; Josh Oxenham (Auckland) 3:01.26, 2; Charlie Makea (Napier) 3:02.88, 3.
Under-17: Alex Barke (Queenstown) 3:05.96, 1; Finn Parsons (Rotorua) 3:06.39, 2; Blake Ross (Auckland) 3:07.10, 3.
Under-15: Marcus Blair (Christchurch) 3:41.41, 1; Max Caulton (Queenstown) 3:42.25, 2; Toby Meek (Dunedin) 3:44.27, 3.
Sport: Harry Chapman (Christchurch) 3:08.72, 1; Ben Friel (Christchurch) 3:09.37, 2; James Carley (New Plymouth) 3:17.41, 3.
Masters 1: Dane Nimmo (Rotorua) 3:14.62, 1; Ben Thomson (Auckland) 3:50.10, 2; Bruce Davey (Auckland) 4:34.62, 3. Masters 2: Bevan Adlam (Queenstown) 3:26.22, 1; Brendan Clarke (Wellington) 3:42.47, 2; Vaughan Love (Queenstown) 3:43.56, 3. Masters 3: Gordon Stillwell (Auckland) 5:33.12, 1.
Female, elite: Kate Weatherly (Auckland) 3:27.93, 1; Shania Rawson (Tauranga) 3:40.59, 2; Amy Cole (Christchurch) 4:10.92, 3; Melissa Newell (Wanaka) 4:37.10, 4; Sam Berryman (Rangiora) 6:59.73, 5.
Under-17: Kalani Murihead (Wanaka) 4:19.08, 1; Maia Jowlett (Queenstown) 5:16.20, 2.
Under-15: Rebecca Hufflett (Nelson) 5:36.05, 1.
Sport: Ashley Bond (Rotorua) 4:26.96, 1.
Masters: Sarah Beadel (Rotorua) 5:35.30, 1.