The Department of Conservation visited the Somerset dairy farm owned by Craigmore Sustainables in April and May, where the kōwaro - or Canterbury mudfish - was found living in the farm's irrigation spring.
The DOC team netted 72 mudfish, ranging in length from 77mm to 149mm.
Somerset business manager Alex Pattullo said the discovery followed the completion of a comprehensive waterway restoration project over the last two years.
"We have replaced the old diesel irrigation pump with a new electric pump to reduce risk of any chemical leaching or contamination and fenced the site to stock-proof it.
"In addition, more than 2760 native plants consisting of dry woodland shrubs and trees as well as flax and reed plants have been planted at the water edge."
Pattullo said the planting would ensure a regenerating native bush block around the site, providing shade, shelter and food for many native and endangered species.