But the six-week window to digest "complex" details has angered agricultural and environmental communities.
Ministry director of water Martin Workman said Environment Minister David Parker was aware of timeframe concerns and had decided to allow for late submissions.
Freshwater quality is the most contentious proposal because of a crackdown on farming practices and an increase in regulations.
Attendees argued this would decrease farming activity, lower land values and negatively affect the export industry.
Many expressed a concern the ministry had not done a thorough impact analysis to uncover the unintended consequences.
Waipahi farmer Ant Logan told policymakers the industry was passionate about protecting New Zealand's waterways, but draft documents were riddled with anti-farming sentiment.
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• Canterbury farmers unhappy with freshwater plan
"We want the same results as you but we feel alienated from this process," Logan said.
"We are not just farmers, we are people of this land ... Don't forget who we are."
On the urban front, the plan to stop the degradation of waterways includes a mandate for councils to have a freshwater plan in place by 2025.
Workman told the crowd he was aware of sewage overflows Queenstown Lakes District Council was dealing with at the moment.
"In this package is proposals on national standards around how those wastewater discharges get managed and what will be required going forward."
Workman said some of the $229 million water clean-up fund would be set aside to help councils.
Submissions officially close on October 17.
On Thursday last week, two public meetings in Southland received "unexpected" farmer interest, as hundreds of people poured into rooms and some had to stand outside.
