Nine major groups have called upon the Government to set tougher standards to clean up the country's waterways.

In a joint statement, the groups – including Forest & Bird, Greenpeace, Fish and Game, and the Environmental Defence Society – set out four policies they argued were fundamental to reversing degradation of lakes and rivers.

They urged the Government to hold hydro-schemes, forestry, agriculture and stormwater management to account and make sure that future policies are made consistent with its proposed new freshwater reforms.

They also supported the stronger pollution limits in the proposed freshwater policy, which were recommended by scientists and based on achieving ecosystem health.

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Specifically, they backed a bottom line for dissolved inorganic nitrogen set at 1mg/L, along with a new index to measure the condition and extent of wetlands.

The groups wanted the Government to take a different approach on setting pollution limits – ensuring that operations couldn't "lock in" their current levels of pollution – and they also opposed the option to make farm plans regulatory instruments.

"Farm plans are a useful tool to support decision-making for farmers and land managers.

"However, clear and effective rules must be prioritised as the best way to achieve the Government's stated goal of measurable improvements within five years," they said.

The other groups were Choose Clean Water, Water New Zealand, The Public Health Association, Recreation Aotearoa and Whitewater NZ.

The Government's package of reforms, currently being put to the public, included new environmental standards that would effectively put the brakes on further intensification of dairy farms and more stringent rules around fencing and nitrogen loss, with some catchments facing having to cut rates by as much as 80 per cent over the next few years.

Councils would have to put the health and wellbeing of water first in decision-making, adopt tougher rules for wastewater discharges, use more monitoring indicators, and ensure swimming spots were at higher standards over summer.

The rural sector – potentially facing a billion-dollar cost - has aired its own concerns over the reforms.

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Last month, Federated Farmers argued the proposals would lead to wholesale land use change to meet what it called unnecessarily stringent targets.

"It becomes very hard to continue economically farming animals or growing vegetables under a regime like this," its environment and water spokesperson Chris Allen said last month.

"The long-term targets for nitrogen reduction, are effectively unachievable in some parts of the country, and will end pastoral farming in these areas."

The official closing date for submissions on the reforms was 5pm tomorrow. However, submissions will be accepted for a further two weeks beyond that date, until October 31.