Melbourne runner Paul Munro’s time of 14hr 37min 46sec beat the previous record of 15hr 30min set by Christchurch runner Marty Lukes in 2013.
Runners in the 160km race set off on Friday morning and the 100km, 80km and 50km events followed at 5am on Saturday.
It is the 10th year of the event, which follows Naseby’s water race around a 10km loop course.
After a "brutal" run through pouring rain, Kendra Breen of Alexandra won the women’s section of the 160km with a time of 28hr 04min 28sec.
"I’ve done the 80km and the 100km here, but nothing like this."
Overnight the track turned to "mud and slush", she said.
"It got so muddy out on the track, especially once the next lot of people started.
"All I want to do is sit down. That’s all I’ve been thinking about."
Organiser Jamie Sinclair said Mr Munro’s effort was "pretty incredible", especially considering the conditions.
"He said it was like wearing roller skates going downhill and he had no traction going uphill."
Out of 42 runners in the 160km event, only 23 finished the race.
"That’s quite a high attrition rate. That’s largely because of the conditions. They slowed a lot of people down."
An ultramarathon runner himself, he said "we’re all crazy".
