The owners of Port Pirie's lead smelter have been fined $35,000 for a series of failures that led to 700 litres of "toxic" sulphuric acid leaking from the plant into waterways and mangroves near the town.

Nyrstar caused material environmental harm by polluting the environment through toxic waste leakage between January 31 and February 2, 2019 — the extent of that harm could not be quantified.

The Environment, Resources and Development Court previously heard the company did not respond for about eight hours as it made "a wrong assumption" that the leak only contained weak acid.

Judge Paul Muscat said the case was not a "flagrant disregard" by Nyrstar and sat at the lower end of the scale.

"An incident of this general nature was not entirely unforeseeable and effective mechanisms to prevent it could — and should — have been implemented," he said.

"The incident was not caused by a single error but a combination of small failures in processes and human error that led to environment harm.

"The harm in this case is to be limited to potential environmental harm that is not trivial."

The acid leak occurred when the systems the Nyrstar had in place to prevent a spillage "failed", with sulphuric acid corroding a wrongly installed valve on the very system designed to safeguard against leakage.

It led to "a slug" of acid filtering into the waterways.

The Environment Protection Authority previously — in seeking a penalty of up to $120,000 — told the court the leak increased the presence of heavy metals in the natural and manmade waterways that were toxic to aquatic life, but it could not be "conclusively proven" that the acid leak was responsible for killing fish, as there was an algal bloom present at the same time.

But Nyrstar previously told the court it had made many improvements to the plant after the incident.

Judge Muscat gave Nyrstar credit for addressing the inefficiencies in its systems.

Nyrstar has also been ordered to pay costs of $5,000.