Other measures under the NPS require regional councils to order efficient use of fresh water by end users, use water quality measures to set freshwater objectives, and "maintain or improve the overall quality of fresh water".
Announcing the policy this morning, Environment Minister Amy Adams and Primary Industries Minister Nathan Guy described the changes as a "critical milestone" to improve water quality.
"Ensuring an on-going and reliable supply of healthy water is one of the most important environmental and economic issues facing New Zealand today," Ms Adams said.
"It is critical that we protect and improve the water quality that we all care so much about."
Mr Guy said the changes balanced economic growth with environmental sustainability.
"It's not an either-or situation - we need both. Primary industries contribute more than 76 per cent of our merchandise exports and largely depend on freshwater, while tourism also relies on the beauty of New Zealand's water bodies."
"We all want sustainable and profitable primary industries. That will mean changes to some of our farming practices, but I know farmers are up for the challenge."
To help councils with the implementation of the new policy statement, Ms Adams was considering applications from regional councils for $1.1m of funding for activities that support regional planning and community participation in freshwater management, with decisions to be announced shortly.
Responding to this morning's announcement, Green Party water spokesperson Eugenie Sage claimed the Government had "pulled the plug" on cleaning up dirty rivers to the point they were safe to swim in.
"Around 90 percent of public submissions called for this. Yet the Government's weak bottom lines have ignored public views and will allow our rivers to become more polluted.
While water quality must be maintained or improved across a region, the minimal acceptable state for rivers was to meet a standard of secondary contact recreation, she said.
This meant making rivers and lakes safe for paddling and wading, rather than the primary contact recreation standard which meant safe for swimming.
With more than half of monitored river swimming sites unfit for swimming, the country was facing a "freshwater crisis", she said.
"The national policy statement allows high levels of nutrient pollution by setting the acceptable level for nitrate - the national bottom line - at a level where it is toxic to fish and aquatic life, rather than at a level which safeguards the ecological health," she told the Herald.
"The Board of Inquiry in the Tukituki Plan Change rejected the approach that the Government is taking in relation to nitrate pollution and set a much tougher limit - the Government should have followed its example."
The New Zealand Freshwater Sciences Society is expected to release a statement on the policy later today.
Irrigation New Zealand has welcomed the announcement, saying that having national bottom lines while allowing for regional and local circumstances would prevent "unrealistic conditions" being set on water quality for irrigation schemes.
"Having everyone work off the same page will mean that resource consent processes will be less onerous and less time and money will be wasted reaching acceptable outcomes," the lobby group's chief executive, Andrew Curtis, said.
The group was also pleased that the updated policy statement seemed to have broadened its measures of water quality and now required a "fuller understanding" of issues which impact a body of water before setting limits.
• Safeguard fresh water's life supporting capacity, ecosystem processes, and indigenous species including their associated ecosystems
• Manage freshwater bodies so people's health is safeguarded when wading or boating (a minimum requirement)
• Maintain or improve the overall quality of fresh water within a region and protect the significant values of wetlands and outstanding freshwater bodies
• Require more efficient use of fresh water by end users, avoid the over allocation of water takes and inputs of contaminants, and to phase out existing over allocation
• Implement the national objectives framework by setting freshwater objectives according to a "specified process" and meeting community and tangata whenua values which include the compulsory values of ecosystem health and human health for recreation
• Use a specified set of water quality measures to set the freshwater objectives (an objective can only be set below national bottom lines in specified circumstances)
• Set limits which allow freshwater objectives to be met and put in place measures to better account for water takes and sources of contaminants, and measure achievement towards meeting objectives.
• Take a more integrated approach to managing fresh water and coastal water.
• Fully implement the National Policy Statement by 2025.