The Freshwater Sciences Society has described the limits for protecting ecosystem health in rivers and streams as "deficient" and noted there was nothing yet in place for wetlands or estuaries.
With rivers, there was concern that the bottom line for nutrients was set only at the toxicity limit for nitrogen, society president Professor David Hamilton said.
"Only one river in New Zealand violates the toxicity limit, yet both scientists and the community know that there are already serious issues from too many nutrients being lost from the landscape and causing progressive decline in river and estuarine health across the country."
Biological invertebrate health measures, a well-recognised metric of river and stream health that had been in use for years, were also absent.
Professor Jenny Webster-Brown, director of the Waterways Centre for Freshwater Management, said she was surprised the standards had left out limits for nitrogen and phosphorous nutrients in rivers to prevent nuisance algae growth.
She also noted no plan to limit what are known as trace toxic contaminants - heavy metals, arsenic and organic contaminants - for ecosystem health.
Associate Professor Russell Death, of Massey University, said the river limits also should have included the key indicators MCI, measuring biological invertebrate health, and IBI, gauging fish health.
There has also been much scepticism about a proposed exception, where the "economic benefits" of existing infrastructure could be weighed against the bottom-line standards.
Professor Hamilton said such cases had to be assessed carefully, and should not be used to promote short-term economic gains. "New Zealand is already paying a high price to address the legacies of past environmental decision-making and cannot afford trade-offs that risk our international credibility in environmental guardianship."
Massey ecologist Dr Mike Joy slammed the proposed exception as an "out clause". "It's a way of weakening provisions that might protect the environment."
A ministry spokesperson confirmed that in these "limited" and "nationally significant" cases, decisions would be made by the Cabinet, rather than councils.
The spokesperson said limits councils needed to set for nutrients would vary depending on local conditions.
A government report card released this year showed that of all river recreational spots measured for faecal pollution and microbial water quality, more than half were unsafe to swim in.
Red = Very Poor, Yellow = Poor, Green = Fair, Blue = Good, Purple = Very Good White = no data.
Source - Ministry of Environment
The above map shows Suitability for Recreation Grade(SGRG) at different sites.
Click on the marker to see the rating for Microbial Assessment and Sanitary Inspection categories.
For further information and to download the data set - http://www.mfe.govt.nz/environmental-reporting/fresh-water/suitability-for-swimming-indicator/suitability-swimming-indicator.html
Some of the locations of the sites are approximate.
