However, Southland Fish & Game and Forest & Bird were pleased with the decision.
Last week, the Court of Appeal decided to dismiss an appeal from Environment Southland which was concerned about the meaning of section 70 of the Resource Management Act (RMA), which sets out restrictions on when a council can include discharge of a contaminant as a permitted activity in a plan.
Environment Southland chief executive Wilma Falconer said, in a statement, the council sought the court’s opinion on Rule 24 of its water and land plan which sought to allow incidental diffuse discharges from farming activities, such as animal urine, as a permitted activity.
"Environment Southland’s position is that it is doubtful additional resource consents for incidental diffuse discharges would have any additional environmental benefit beyond the land use rules the Southland Water and Land Plan already provides.
"Instead, it will add another layer of bureaucracy and cost for farmers and require the council to resource the significant increase in consents processing that would be needed."
Federated Farmers spokeswoman Bernadette Hunt agreed with her and said they also would not let this lie.
"This impractical decision is a total disaster for Southland farmers and lacks any common sense.
"If 3000 local farmers were to all apply to Environment Southland for a consent at the same time it would completely overload the system.
"It would become an expensive and bureaucratic box-ticking exercise that adds nothing but cost and complexity for farmers, for no environmental gain."
She said the news came at the worst time as farmers across the region were already under pressure and stress due to adverse weather conditions which were negatively impacting them.
However, she wanted to assure farmers they did not need to worry.
"There’s a process to go through now before any changes come into force, and that will take time in any case.
"Therefore there are no immediate implications for farmers to be concerned with."
Southland Fish & Game resource management officer Jacob Smyth said the court decision was not a surprise as it was the third court to find that the plan identifying discharge as a permitted activity would not achieve the improvements needed to meet national requirements for Southland's heavily degraded rivers.
"The Environment Court has found that Southland's rivers have significantly deteriorated, largely due to farm-related contaminants.
"This decline had occurred under Environment Southland’s lenient rule framework.
"To fix this, Environment Southland must tackle the root cause."
A Forest & Bird spokeswoman said the decision upheld a critical environmental concept in the RMA, that contaminants could not be discharged where they would have significant adverse effects on aquatic life.
"Where waterbodies are degraded to the point that discharges are having significant adverse effects, council oversight of those discharges through a resource consent process is appropriate, so that contaminants can be managed down and water quality improved.
"Southland Regional Council’s response to losing on this issue for the third time is a knee-jerk reaction that prioritises pollution over freshwater health."
