The Environment Protection Authority says it is prosecuting Nyrstar Port Pirie for causing serious environmental harm.
The complaint alleges that the company polluted the environment between January 31 and February 3 last year.
The authority said Nyrstar had "polluted the environment by discharging, or failing to prevent the discharge of, about 700 litres of sulphuric acid from its site into First Creek at Port Pirie".
The authority said this had resulted in potential environmental harm and created conditions for fish and other flora and fauna species in the creek.
The offence is covered by of the Environmental Protection Act 1993.
In a response to the summons, Nyrstar confirmed receiving a court order after an investigation by the authority into an acid spill on January 31 last year.
A spokesman said the company had taken the steps necessary after the incident to ensure it would not be repeated.
"Following the incident Nyrstar implemented new processes and alarms," said the spokesman.
Due to the legal proceedings, the company will refrain from further comment.
The matter will be heard in the Environment, Resources and Development Court of South Australia.