This included a rare longfin species and 30 fish.
In April this year the ammonia was found in a four kilometre stretch of the Kaputone Creek in the suburb of Belfast, along with the dead eels and fish.
After an investigation lasting several months, the regional council laid criminal charges against Polarcold Stores Limited.
The company faced a maximum $600,000 fine.
It had yet to enter a plea on a second charge of releasing ammonia gas in to the air.
An individual also faced two charges of illegally discharging the chemical.
They will next appear in court on 19 December along with the company.