The paddock surrounding the flaxlands, near to the Ruamahanga, floods three to four times a year, and stopbanks have been built to try to keep the water in to promote the growth of the wetlands.
Farmer Grant McGhie, who has worked on Wairio Station for more than 25 years, said the paddock left stock stranded during flood and he wanted to see the native flax and cabbage trees saved.
Mr McGhie said he has seen teal, paradise and mallard ducks in the wetlands and is hopeful as it grows it will draw in more wildlife. "It doesn't look like a lot at this stage but you can see the potential that's there."
The covenant was put in place by QEII National Trust in partnership with Landcorp, which supports 120 farms with areas containing covenants around the country - it is Landcorp's first in Wairarapa.
National manager Phil McKenzie said Landcorp was lucky to be working with farmers who do what they can to protect the environment they work in, and hope to leave something better behind.
"It creates a better area to work in, a better life ... the days of bulldozers and matches everywhere are behind us," he said.
"I think farmers always have been concerned about the environment they live in, they don't want to create scorched earth."