The discharge resulted from a 40cm split in a 60m pipe feeding an irrigator, where effluent was found pooled when investigators tracked the source of the leak.
It emerged the irrigator had been unreliable over the weeks before and had stopped often after becoming blocked, with Mr Standish having to cut away a length of pipe at one stage.
When the second leak was discovered, farm staff quickly reacted and Mr Standish built a bund to protect the nearby wetland.
"The cause of the discharge was the failure of Armer Farms to adequately ensure a system for checking their irrigator and ensuring that any damage to it resulting in discharge in effluent ought to have been picked up much sooner than it was," Judge Robert Wolff said yesterday.
"The cause of the accident was a split pipe ... but primary steps could have been taken to ensure there was a more rigid process in place."
He did not accept a view submitted by the company's lawyers that the breach was a "one-off event".
"It was an inadequate system, or there was no system at all, to ensure that the irrigator was working adequately."
The company, which was charged with unlawful discharge of dairy effluent and with the exception of a warning in 2003 had a clean record, was due to take the case to trial before pleading guilty on May 31.
Judge Wolff acknowledged the prosecution would cause Mr Armer embarrassment given his standing in the dairy industry - something the defence team had argued had already been an element of penalty.
A spokesman for Fonterra said Mr Armer had advised of the breach "some time ago", as well as the "general controls he has in place and actions taken to fix the problem".
The system had since been replaced.
Bay of Plenty Regional Council pollution prevention manager Nick Zaman told the Herald he hoped the sentence sent a clear message to farmers.
"It is quite unfortunate that this case has had to come to court, as it was something that quite clearly could have been avoided."
