About 2600 dead eels were recovered from the Low Burn Stream and nearby tributaries in February.
Environment Southland resource management manager Donna Ferguson said there were likely more eels in areas they were unable to access and some would have been washed away.
Evidence collected during the investigation suggested the deaths were caused by a contaminant in the waterway, rather than a disease, she said.
Hokonui Rūnanga kaiārihi taiao (environmental lead) Riki Parata said the contaminant that killed the tuna (eel) likely affected many other species living in the rivers and streams surrounding the area.
"Because tuna are long, they got caught up in willows and roots and bank wads.
"I think this really needs to be highlighted a bit more — tuna were the only thing that were left."
They had also found some dead kōura (crayfish) and trout.
"We’re devastated and we’re pretty saddened by the whole bloody thing.
"It’s totally unacceptable, there’s no way this should be happening in this day and age and it should not become a normal thing."
He was frustrated by the news the deaths had been caused by a contaminant.
"Even if it was done purposefully or not, it’s still negligence."
There were multiple community groups, iwi groups and farmers doing their best to protect these waterways, and had been for many years, he said.
"It just seems to be a very select few that’s doing quite a bit of damage."
As the investigation was ongoing, he could not speak on what caused the contamination, but felt strongly about finding the source and educating on the importance of protecting waterways.
"I think there should be larger penalties for people who do these kinds of things because that is a hell of a lot of tuna and a hell of a lot of life that has been wiped out from a stream that needs to rebuild — and it will take many years for it to be rebuilt."
It was one of the last remnants of the naturalised wetlands left, Mr Parata said.
"Our wetlands have been wiped out and what’s remaining are these streams and drains. So we can’t be treating them like sewers and disposals any more."
Ms Ferguson said the investigation would "take some time", and to preserve its integrity it would not provide any more updates until it was complete.
She could not confirm whether the waterway had been cleared of the contaminant and remnants might still be present as it worked its way through the system.
"The Low Burn stream has been severely impacted and is now in poor ecological health.
"We are speaking with experts to understand the longer-term impacts on the stream and how long the ecosystem might take to recover."
