Council northern area manager Nathan Heath said a resident had organised an excavation to open up the mouth, which was already "a bit open".
Most rivers and streams on the east coast of the North Island had a tendency to "swell up" due to deposits like sand over time, he said.
The Hine Rauiri stream was no exception.
"The mouth of the stream is probably 100m away from the outlet and the drain behind it collects. So if we open the outlet, more water flows in and affects the wetland.
"Once the water level rises on the wetlands, the drain fills up and may lead to overflow into residential properties," Heath said.
"We don't really have a concrete method to solve it at the moment as there are conflicted outcomes, but we are investigating options for design and location."
The council was getting a recommendation from ecologists and internal engineers from Hawke's Bay for technical advice, he said.
One of the options being discussed would include placing a weir — a small wall-like barrier — that would help retain a significant amount of water in the wetlands.
"We are well aware of the Mahanga community's concerns about the flooding of property from the wetland and we are working with Wairoa District Council and the Department of Conservation locally to try to resolve this."
Council policy and regulation manager Katrina Brunton said residents should not take matters into their own hands.
The Department of Conservation had an interest in protecting the wetland values of the Mahanga Wetland, said Doc east coast operations manager Chris Visser.
DoC would continue to work with the local councils to support an engineering solution to management of the water level of the wetland.
- Gisborne Herald