Farmer Earl Mitchell raised the alarm after spotting the couple's van almost fully submerged in the water from the Waimana River shortly after 11am.
Waimana Rural Fire Party chief Bernie Clark said firefighters arrived to find the van almost completely submerged.
"The van was stuck and there was only about six inches [15cm] of the roof showing.
"We weren't too sure if they had got out or not ... We put our own people at risk to try to save someone who might not even be there."
Mr Clark said trying to drive through the flooded gorge was "a bit stupid".
The man and woman, thought to be in their 30s, climbed a bank to safety and were huddled together when Mr Mitchell found them.
He rang his neighbour, Waimana Helicopters pilot Robert Fleming, who flew the pair to Taneatua and later to Whakatane Hospital.
Mr Fleming said they were extremely lucky not to be swept away by the river.
"They're fortunate they didn't get taken with the flow of the water. They must have had to swim to get out [of the van]."
They weren't the only motorists affected by the floodwaters in the Bay of Plenty during a weekend on which than 300mm of rain was dumped in some areas.
Thousands of people - many going home from Gisborne's Rhythm and Vines music festival - were trapped in and around Whakatane and Opotiki after rain and slips blocked highways.
Several smaller roads remained underwater last night, isolating residents in places such as Taneatua and Waimana.
Senior Sergeant Michael Lander of Gisborne police said the closures, including the main route north from the festival which was blocked for most of yesterday, had created a headache for travellers.
He said about 30 per cent of the 29,000 people who attended Rhythm and Vines over its three days came from Auckland.
Transport Agency central region manager Anthony Frith said the timing of the closures was unfortunate.
"It's obviously quite a frustrating situation for people - it's really the last thing you want on New Year's Day."
Waimana resident Julie Kururangi was stranded in Opotiki with her husband and 8-year-old daughter yesterday and said the town was packed with campers returning from the music festival.
"We're lucky. We're with our in-laws, but we'd like to go home."
MetService severe-weather forecaster Mark Pascoe said Waimana, about 27km southeast of Whakatane, was one of the worst-hit areas in the weekend storm.
It had 390mm of rain - more than its monthly average - in 48 hours.
Yesterday, the heavy rain moved to the central North Island.
Waiouru had 32mm of rain in less than an hour, and police reported flash flooding across State Highway 1 between Mangaweka and Ohingaiti, south of Taihape.
Waimana farmers Faye and Bernie Clark moved their herd of 400 cows to higher ground on Saturday to avoid floodwaters which have covered almost all their 145ha farm.
Mrs Clark said about 250mm of rain had fallen in the past few days.
The heaviest downpour was on Saturday night, and by yesterday, the water was so deep she could not see the fences.
Mr Clark said it would take weeks to clean up after the floods.
Fire Service shift manager Jaron Phillips said one of the weather-related calls received yesterday was from a mother in Waimana who was concerned about rising floodwaters in her backyard.
She was home alone with three young children and her husband was trapped in a ute by floodwaters and unable to get home. Firefighters were unable to reach the woman but Mr Phillips said the family were safe.
- additional reporting: APNZ
