Waste from a milking shed is the cause of a contamination to Winton Stream in Southland.

Environment Southland confirms over-irrigation of dairy shed waste has made it dangerous for animals or humans to come into contact with water from the stream.

Compliance manager Simon Mapp said the effluent in the stream is obvious.

"The officers that actually attended on the day - they could see a visible difference in the creek as far as three kilometres downstream from the discharge."

"We do know that it's the result of over-irrigation of dairy shed effluent from a dairy farm," said Mapp.

People are being warned to stay clear of the stream.

Dog owners are being told not to let their pets drink the water, and people who use the water for household use should stop.

Further test results are expected by the end of the week.

Mapp said it's too early to say how much damage has been done to the stream.