A Southland meat processing company has been fined more than $50,000 for allowing wastewater to flow into a waterway twice in two days.

Blue Sky Meats New Zealand had to accept ''a high degree of carelessness'' over the discharges on October 9 and 10 last year, Judge Brian Dwyer said when sentencing the company in the Environment Court at Invercargill yesterday.

The company had earlier admitted effluent sprayed on paddocks near its plant at Woodlands ran into a swale and entered a field tile drain entrance Blue Sky Meats did not know was there. It then entered a tributary of the Waihopai River.

Because the company's plant effluent storage capacity was inadequate, it was necessary to spray effluent daily regardless of whether the weather conditions were suitable, Judge Dwyer said.

Field tile drains were a regular item in Southland, he said, and Blue Sky Meats staff ought to have known of the drain entrance.

It was accepted 1000cu m of effluent entered the waterway and there were ''obvious and significant'' temporary environmental impacts on the waterway.

Environment Southland, which brought the prosecution, sought a starting point of a fine of $60,000 on each charge, while Blue Sky Meats, suggested a $20,000 starting point.

Judge Dwyer said he was basing his sentence on a similar case involving another Southland meat processing company in 2013 involving an estimated discharge of 300cu m of effluent.

He fined Blue Sky Meats $25,125 on each charge, plus court costs and solicitors' costs, ordering that 90% of the fine be paid to Environment Southland.

The judge noted the company had donated $10,000 to the Friends of the Waihopai Trust as a gesture of goodwill.

He also granted Environment Southland's application for an enforcement order requiring Blue Sky Meats to take steps within 30 days to improve its effluent disposal system and increase storage capacity.

Michael Parker, for Blue Sky Meats, said a $30,000 pilot scheme upgrade was expected to be operational in a few weeks.