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Harrison Spraying Services was sentenced on April 21, after earlier pleading guilty to spilling an agrichemical onto land near a stock water race which runs through Mt Somers village.
Environment Canterbury said a truck driver for the company was mixing a tank of the chemical with water from the race when it overflowed.
The regional council estimated between 600 to 1000 fish died along a roughly 6km stretch of the waterway.
That included brown trout, common bullies, native kōkopu and kēwai (freshwater crayfish).
Inspections by staff about six months after the incident found that the discharge was still having an effect, with an absence of fish species downstream from where the incident occurred.
At this stage, ECan said the long-term effects on the stock water race were unknown.
Spokeswoman Janine Holland said the fine was a satisfying outcome and should serve as a reminder for businesses that they had a responsibility to protect the environment.
"Ignoring these responsibilities can have devastating and far-reaching impacts on our aquatic species," Holland said.