Southland's regional council will use emergency powers to open Waituna Lagoon to the sea after weeks of unusually high water levels.

Environment Southland said the lagoon near Invercargill had stayed above 2.2m since late July, affecting nearby roads, paddocks and farms.

For the past five days it had been above 2.3m, the council said.

General manager integrated catchment management Lucy Hicks said the lagoon's opening should reduce pressure on surrounding land and lower the risk of ecological damage in warmer months.

"There are trade-offs in opening the lagoon at this time of year," she said.

"We need to reduce the risk of nutrient-rich water sitting in the lagoon and fuelling algal growth, while also considering spring and summer growth for Ruppia and other aquatic plants."

Diggers will carve a channel through the gravel bar separating the lagoon from the sea so the water can drain out.

Hicks said the lagoon could not be closed mechanically once it was open.

"It requires the right combination of wind and sea conditions to push gravel back into the channel that we will be creating with the digger."

Waituna Lagoon is part of the internationally significant Awarua-Waituna Wetlands.

It has previously been plagued by algal blooms and deteriorating water quality.

The council used emergency powers twice in 2024 to open Waituna Lagoon to flush out cyanobacterial bloom.