Fish and Game is upset at work it says farmers are planning on land encircling Lake Poukawa south of Hastings.
During heavy rain, the 270-hectare lake overflows into neighbouring land.
Fish and Game says the temporary wetlands it creates are significant, supporting the endangered bittern and a range of ducks including shovelers, which use them as a major flocking area.
The group says farmers want to surround the lake with an embankment and drain the peat soil on its edge.
Fish and Game's freshwater biodiversity officer John Cheyne says he understands the need for efficient farming - but there must be a compromise.
"The ephemeral wetlands can be grazed and crops grown on them for six months of the year and the other six months of the year they're wet. Everything wins - but if a bund goes in with a pumping situation, the wetland habitat is totally destroyed.
Mr Cheyne says 90% of New Zealand's original freshwater wetlands have been drained.
One of the biggest farmers in the area is Brownrigg Agriculture.
Joint managing director Jonathan Brownrigg says water on surrounding farmland is drained back into the lake but the peat is not drained.
"We're going to great lengths to preserve the wetland, preserve the peat. The whole area here in the Poukawa basin is very special and of great value and significance."
Mr Brownrigg says he is happy to discuss with Fish and Game any worries or plans it has about and for the lake.