Forest & Bird says it plans to take legal action against Auckland Council over its plans to let stormwater into streams and the sea.
The council has granted resource consent for its own Healthy Waters unit to divert and discharge stormwater across the region for the next 35 years.
Forest & Bird is appealing the consent, saying it lacks clear rules that would stop stormwater from damaging streams, the coastal environment and native wildlife.
The conservation group's Auckland regional manager, Nick Beveridge, said the consent allowed stormwater to be discharged from existing networks and any new networks developed in the next 35 years.
Mr Beveridge said stormwater could contain heavy metals and other contaminants that pollute streams and the sea.
"This consent is a serious concern because it doesn't set clear requirements to make sure the council does not damage waterways, the marine environment, or native fish and sea life."
The council's stormwater system channels rainwater that is collected from private properties, public reserves and roads.
The system includes 25,000 outlets, 6000km of pipelines and 900 stormwater detention and treatment facilities.
Many of the pipes dump stormwater into streams, rivers or the ocean.
Mr Beveridge said Auckland had some important ecological areas with rare birds and sea creatures.
"There could be stormwater discharges from new developments, such as big subdivisions, and we're worried.
"There are not enough conditions in the council's consent to be sure the coastal environment and significant ecological areas won't be harmed."
Consent will improve environmental controls - Healthy Waters
The council's stormwater network is run by a unit called Healthy Waters.
Its general manager, Craig Mcilroy, said stormwater runs off every time it rains, over land or though pipes and discharges into streams, estuaries and the sea - whether there was a consent or not.
"Healthy Waters is seeking to improve the quality of stormwater discharges by applying for a regionwide network discharge consent.
"A regionwide consent will enable cost savings, efficiency, consistency and improved environmental controls."
Mr Mcilroy said other benefits include replacing the existing 116 consents across the city with a region-wide consent.
"Healthy Waters supports the decision of the independent planning commissioners to grant resource consent to the publicly notified application, and looks forward to working with Forest and Bird and the other Environment Court appeal parties to fine tune the details of the consent."