The group wrote to Eugenie Sage asking for "greater protections" for the Waiau catchment.
In the letter, Guardians chairman Darryl Sycamore said he believed the exclusion of the Manapouri Power scheme in Section 3.22 of the national policy statement for freshwater management was made despite the concerns of conservation leaders including the Guardians, Environment Southland, iwi and the local community.
He believed the effects of the Manapouri hydro scheme were generally overlooked "despite it being clear that the river system and estuarine environment are being adversely impacted".
"These effects are a direct consequence of the schemes operation in particular the power schemes diversion of in excess of 90% of the rivers flow."
Mr Sycamore said the consumptive take associated with the Manapouri scheme would make it unsuitable for exemption.
His concerns reiterated those of the Waiau Rivercare Group, which recently launched a petition asking the Government to revise the matter.
Waiau Rivercare Group chairman Paul Marshall described the Government’s decision as a "death knell for a river already choking to stay alive".
The petition, listed on Parliament’s website, closes this weekend.
Minister of Conservation Eugenie Sage said she was aware of the concerns raised by the group.
Following a meeting with the group leaders last year, she raised their concerns with Minister for the Environment David Parker during the development of the national policy statement for freshwater management "to try make sure the changes maintained and enhance the health of the Waiau catchment".
"I am continuing to see what can be done in this area and am happy to meet with the groups again," Ms Sage said.
