A piggery farm near Te Aroha is facing prosecution over repeatedly discharging effluent into a stream.
However, it could be at least a year before the Waikato piggery appears in court.
And while the "volume and frequency" of the discharge has decreased, effluent is still leaving the farm.
Waikato Regional Council compliance manager Patrick Lynch said the effluent discharge happened over a long time frame and in large volumes.
A video taken by council staff on 2 August showed effluent overflowing from a holding tank into a stream after locals reported the stench four kilometres downstream.
Landowners had been warned that piggery effluent has entered the Patuwhao Stream, which flows to the Waihou River. Because of this, Lynch said there would be faecal bacteria, ammonia and high nutrients in the water.
Lynch said the activity was unlawful and an emergency Environment Count order stated the activity must stop. He said staff had been carrying out regular inspections of the site.
"There has been some improvement. The volume and frequency of the discharges has decreased, though there is still work to do and we will continue to monitor activities on the site."
This week, Waikato Regional Council went a step further by taking out a prosecution against the piggery under the Resource Management Act (RMA).
Lynch said it came as a result of an active investigation by the council into alleged ongoing, uncontrolled and unauthorised discharges to both land and water over the past six months.
He said an average court case would take a year, although some were still unresolved after four years. And in that time, the piggery could continue to operate.
"It shows there are some limitations under the RMA. We completely understand that the community would think, 'Why can't you just shut them down?' But the RMA actually doesn't allow for that.
"It's ultimately a conscious decision for the people involved to become compliant. They have to do that themselves. We are just trying to use the various tools available to us, to coerce that decision."
Lynch said the circumstances made it one of council's more serious prosecution cases. If the prosecution was successful it could result in a criminal conviction, but more likely a fine of up to six figures.
Lynch said the council anticpated dealing with the piggery for years to come.