The Resource Management Act (RMA) will be amended within 12 months to enable regional councils to more quickly implement water quality and quantity limits.
The changes included controls on the excesses of some intensive land use practices, as well as ensuring wetlands and estuaries were better protected, Mr Parker said.
A report discussed at the Otago Regional Council last month showed 40% of Otago water bodies were considered "poor'' or "fair'' in terms of overall health.
Otago Fish and Game environmental officer Nigel Paragreen said the announcement was big step in the right direction of aiding a "worrying trend of degradation'' which needed to be "urgently halted''.
He hoped the programme would add to discharge quality standards already coming into effect in 2020.
"Sediment discharge is probably the biggest issue for water quality in many of our catchments.''
Regional council chairman Stephen Woodhead said he supported the minister's focus on at-risk catchments. He welcomed the RMA changes, as plan change timeframes were too slow, costly and ultimately affected the council's ability to adapt in a timely manner.
However, real change relied solely on the actions of urban and rural landowners, he said.
Cr Gretchen Robertson said the Government had listened to the public cry for better water quality nationally.
"Otago is a region that prides itself on high quality water resources and enjoys many economic benefits from these. We also have some serious water quality issues to face up to.''
Manuherikia farmer and water leader Gary Kelliher said he had not had time to digest the information yesterday in terms of how changes would impact the setting of minimum flows.
Allowing a quick process for plan changes was good as long as they were robust, focused on problem catchments and did not paint all catchments with the same brush.
The work programme sets out a new approach to the Maori/Crown relationship that will acknowledge Maori interests in fair access to water to develop their land.
Federated Farmers water-quality spokesman Chris Allen said the five-year goal was "really ambitious''.
In the past 10 years, farmers had come a long way improving water quality and the pace was increasing.
National environment spokesman Scott Simpson said the announcement was "underwhelming''.
"Today's announcement is just another working group that kicks water issues to touch until 2020... coincidentally this is when the Government's Tax Working Group proposals of a series of new environmental taxes would take effect.''
jono.edwards@odt.co.nz
