Fonterra will from now on be checking the effluent systems of all the farms supplying it with milk every year.
After being tested in a pilot scheme in Waikato, a programme for every farm, every year is being rolled out throughout the country.
The aim is to improve compliance with regional council dairy effluent rules.
A Clean Streams Accord survey earlier this year showed 15% of farms were significantly breaching the conditions.
Farms that don't measure up in the annual checks will be referred to a team of sustainable dairy specialists, who will help the farmers to work out a plan with a deadline for fixing their effluent problems.