Conservationists say farmers must start paying for the pollution they produce or the country risks many more of its significant waterways being forever lost.
Some 200 people attended the bi-annual National Wetlands Symposium in Invercargill heard on Wednesday.
Conference delegates travelled to Waituna Lagoon, near Invercargill, where highly concentrated nutrients from farms are killing the lagoon's ecosystems.
Guy Salmon, executive director of the Ecologic Foundation, which promotes sustainable development, says not enough is being done to make farmers carry their share of problems associated with intensive farming practices.
"The dairy farmers have been allowed in without anybody taking a close look at their impacts on the environment and now we're finding after a few years that actually those impacts are quite serious.
"The dairy farmers are acknowledging that they are having an impact but ... unless they are facing a price signal for their pollution, it's not going to be all that easy to get everybody to fix it up," Mr Salmon says.
The Parliamentary Commissioner for the Environment, Jan Wright, released her report into the state of the country's waterways on Tuesday, saying there is now no question that the intensification of farming in the catchment surrounding the Waituna Lagoon is contributing to its demise.
'It's not all over yet'
A Department of Conservation wetland ecologist, Hugh Robertson, says all is not lost at the lagoon.
"We see Waituna Lagoon as still one of the most significant coastal lagoon systems in the South Island. It still maintains a healthy native fish community and also an intact aquatic plant community, high cultural values and is increasingly used for recreation.
"So it's not all over yet and we are hoping we can put some programmes in place that can restore it and maintain for the long term," he says.
The lagoon is particularly significant to local iwi. Ngai Tahu representative Dean Whaanga says the iwi wants intensive farming stopped. He says a rahui, or ban, should be put in place.
"That's a tool used to say we are going to stop what we are doing until we figure out what the problems and the issues are until the environment sorts itself out again," he says.
But local dairy farmers are incensed by the suggestion they are not doing anything to mitigate the problems of intensive practices.
A third generation dairy farmer, Gerald Spain, says Guy Salmon's comments at the conference were misleading and local farmers are spending hundreds of thousands of dollars to protect the health of the lagoon.
"We might have a part to play in it but we are definitely not the whole picture," he says.
Mr Spain says local farmers have formed a new group, Waituna Farmers United, to do as much as is practicable for the benefit of the lagoon.
Each farm has been visited and a plan drawn up to bring it up to scratch. A year later each farm will be rechecked against its plan.
The Government has a new $700,000 plan to restore riparian strips and collect sediment from the lagoon over the next several years.