Federated Farmers Southland president Allan Baird has admitted his farm is responsible for the effluent spill into the Winton Stream.
Environment Southland is investigating after a "significant volume" of effluent went into the waterway from a dairy farm in October.
The spill increased E coli levels in the water and the local council warned people to avoid contact with the stream and keep their dogs away.
The stream has since been cleared for use.
Mr Baird said there was a fault with his effluent irrigator, which meant it pooled in the paddock and ran down into the river.
"A number of circumstances all rolled together and a reasonably new staff member was restarting the irrigator - and it was the technical part of the irrigator," he said.
"It never activated all parts, and basically meant the hose didn't wind in, and the irrigator was stationary for a period of time."
Because of that, the water pooled on the surface and ran into a farm drain, which took the effluent into the Winton Stream, Mr Baird said.
Mr Baird said the aftermath highlighted the need for better clean-up processes.
He called Environment Southland as soon as he discovered the spill, but said he needed better materials to clean up.
"We always carry bales, (baleage) so I put a bale in the drain as well and then looked to hold any fluid back. A little more robust material could have been helpful, I was a little surprised that the council didn't have a little bit more material on hand to help in the first instance.
"It wasn't until the second day that a staff member came along with a little more substantial equipment to secure that creek flow."
There are more than 1000 dairy farms in Southland, and some additional resource would be a good idea, said Mr Baird.
"The Fire Service carry material for fuel spills, but when an effluent spill occurs - what is the right level of infrastructure?"
Environment Southland policy director Vin Smith said they could not comment on the investigation into the effluent spill or the clean up.
He said while it was the farmer's responsibility to clean up, the council could step in.
"We'd get sucker trucks, we'd get booms in place, we'd get actions occurring to address the particular issue as quickly as possible."
He said the council talked to farmers about what the best process was.
"Every issue is different, it has its own nuances, it could be that you may need to dig a cut off drain ina paddock to actually divert contaminant or effluent over a paddock into a drain."