The Otago Regional Council is looking to work more closely with farmers in the Kakanui River catchment after a study found a deterioration in water quality.
The 10-month study found that levels of phosphorous, nitrogen and E-Coli were above recommended guidelines in the North Otago catchment area.
Council chairman Stephen Woodhead says the results are not too surprising as stock numbers in the area, especially dairy cows, have increased since the land was irrigated in 2006 and soil types there have poor filtration qualities.
However, he says some farmers in the Kakanui catchment need to upgrade their effluent storage capabilities, while others need to fence their stock off from waterways.
The council will meet local farming leaders to discuss ways of stopping the increasing leaching of nutrients into the area's waterways.
Kakanui dairy farmer Leigh Hamilton, who also chairs North Otago Irrigation Ltd, says the report is being taken seriously.
"This is the first that we're aware of the water quality being degraded, and it's something that we care about. We don't like that happening, we want to understand why that's happening.
"We have systems on farms to monitor what's happening there and to make sure that we are looking after our water quality, but there's probably always more we can do. So it's just a reality check for us really to try to get a handle on what's happening."
Mr Hamilton says farming has intensified in the Kakanui catchment since large-scale irrigation was introduced, and the challenge for farmers is to manage their operations so that the water they are applying is not running back into waterways.
He says North Otago Irrigation is investigating what measures its 70 farmer shareholders can take to reduce run-off.
"It's the thing that concerns us the most as an irrigation company. We appointed an environmental manager a couple of years ago because we just know these are the things that we want to be able to deal with.
"It's about how we feel about being an irrigation company and how we feel about being farmers. We want to do the right thing and we're going to be open to facts and work with the people who are trying to make that happen."