The lagoon has been running very high for several weeks, sitting above 2.5m and affecting communities, roads, paddocks and farming activities in the area.
General manager integrated catchment management Lucy Hicks said council scientists were working with others to assess the effects of consistently high water levels on ecological health.
"To prevent ecological harm, we have made the decision to open the lagoon, which will also support the community."
The lagoon will be opened by diggers removing gravel from the bar starting today until a channel is formed and water from the lagoon can flow to the sea.
The opening needs to be carefully co-ordinated to occur when conditions allow it to be done safely and effectively.
"Opening the lagoon at this time of year has its pros and cons.
"We’ve considered the timing, the need to flush nutrient-laden waters to prevent sustained algal growth, while considering the needs of Ruppia and other macrophytes which germinate and grow in spring/summer.
"The goal is by flushing nutrients and sediment, this opening will help ‘reset’ the lagoon so that we can reduce the frequency of openings for ecological health.
"We will be doing all we can to increase the odds of the lagoon closing prior to summer. Historically, it has required the right combination of wind and sea conditions to push gravel back into the channel that we will be creating."
