Farmer-led efforts to clean up Golden Bay's Aorere River catchment have been a poster project for the dairy industry.
OPINION: The Aorere Catchment Group initiative was launched in 2005 after high pollution levels from the river meant Golden Bay marine farmers could harvest less than a third of the time.
Dairy farmers' work to keep effluent from waterways has improved the quality of the Aorere and its tributaries, winning national and international recognition.
In March this year Federated Farmers Golden Bay dairy chairwoman Sue Brown was named as one of six Landcare ambassadors for heading the project.
So it's disturbing for dairying and marine farmers that high bacterial readings have again been found in mussel farms off the Collingwood coast.
The marine farmers say tests show the raised E. coli counts in recent months come from dairy effluent, and were at levels that would have shut the farms if harvesting was under way.
A stock crossing, permitted under council rules, has been identified as the source of one dairy discharge.
Another has been attributed to stock grazing on a road verge, but the source of two other discharges remain unidentified.
It's particularly worrying because there is no doubt Aorere farmers have put a lot of time and money into pollution control measures to keep stock out of waterways and improve effluent storage and treatment.
That problems have resurfaced raises questions over the ability of the industry to ensure its rapid growth is matched by environmental safeguards.
The voluntary Dairying and Clean Streams Accord, an agreement between dairy giant Fonterra, the Government and regional councils, is now at the end of its 9-year life.
Environmental groups argue it has seen slow and inconsistent progress. The industry says it has led to big improvements, such as bridges and culverts for stock crossing waterways.
Figures show a stubborn percentage of farms - 11 per cent in 2010-11, 16 per cent the year before - have significant non-compliance with effluent rules.
There are also questions over inconsistent regional council consent policies and how well they are monitoring farms.
In Tasman, for example, treated effluent is allowed to be discharged into waterways as a discretionary activity. Other regional councils prohibit it.
At a national level, time may be running out for voluntary measures.
A tougher regime to replace the accord is being discussed and the courts will be asked to decide on the Horizons (Manawatu-Wanganui) Regional Council plan that could set nutrient limits on farm runoff.
The Government has also asked councils to review freshwater management.
Dairy farming is one of our most valuable industries, but if the actions of a tardy few spoil the environment there will be no winners.
The industry has had nine years to get its house in order; now it's time for stronger measures.