The Waikato Regional Council manager of investigations and incidents Patrick Lynch says he expects a 300 – 400 per cent increase in prosecutions of dairy farms this year.

Earlier this month, H & S Chisholm Farms Limited in Putaruru was fined almost $60,000 for two discharges of effluent into a stream flowing into the Waipā river.

The regional council was alerted by a member of the public who said the Waipā Stream looked contaminated.

When investigated the council found an effluent holding pond overflowing into the nearby stream, and on a return visit found that dairy effluent was still entering the stream from an effluent irrigator used on the farm that had been left on.

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Judge Melanie Harland said the company's response to the incident was exemplary but it should not have occurred.

"Dairy farmers in the Waikato region have had ample time to understand what is required to lawfully manage dairy effluent."

Lynch said the regional council has prioritised resources to focus on high risk farms, which he said was 19 per cent of farms in the Waikato.

"We're now really focusing our monitoring those farms that we just know have got really high risk systems, so these are the seven days or less [effluent] storage.

"What we're starting to find is a lot of really serious breaches.

"That means we've got about 800-ish dairy farms in the Waikato that, if you had a week of wet weather which happens a lot in the Waikato, then [they're] going to be unlawfully discharging effluent into the environment."

Waikato farmer and Waikato Federated Farmers chair Ben Moore built a new 800,000 litre storage pond after consent for his old system ran out.

He said it gave him about 50 days storage, which was less than the recommended best practice of 90 days.

"The trouble is this 90 days storage is sort of plucked out of thin air. What's as important as storage is spreadable area. We've got 40-50 days [effluent storage] that we can spread over 60 hectares.

"If you've got 90 days storage and you've got 6ha of spreadable area, then what are you going to do to that 6ha?"

Moore said farmers were trying to protect their brand and needed to be seen to be doing the best thing.

He said farmers across the board were pretty disappointed when these breaches occurred.

"All you've got to do is jump on Twitter and have a look.

"The majority have done the right thing," Moore said. "And with generational change, we're getting better at it.

"[But] If there's one key message to farmers it's 'sort your shit out, otherwise it's going to get sorted for you'."

Lynch said 400 of the approximately 800 high risk farms would be visited this year which would likely result in more prosecutions for some.