Mr and Mrs Weller, who farm Crosshill, an 890ha sheep and beef property in the Waimea Valley, were chosen from nine regional winners.
It was the first time a national winner had been named in the competition and the couple were presented with the Gordon Stephenson Trophy, named after the Waotu farmer who started the awards, at the New Zealand Farm Environment Award Trust's sustainability showcase in Hastings.
Mr and Mrs Weller would be "great ambassadors" for New Zealand agriculture, NZFEA chairman Jim Cotman said.
"They are successful business people and strong communicators who will be able to effectively convey their sustainable farming beliefs and actions to a wide audience within New Zealand and beyond," he said.
The couple were also recognised by Federated Farmers at the organisation's Cream of the Crop awards in Rotorua.
It was important to celebrate success in agriculture and acknowledge those who displayed excellence in their custodianship role of the land, water and other resources, chief executive Conor English said.