It is public land which is managed by Parks Victoria and is surrounded by farmland, golf courses and residential housing.. Because of its relatively small size and isolation from the rest of the Lake Connewarre wetland complex it is threatened by edge effects, including pollution from stormwater run-off.

[5] A report by Neville Rosengren for the Save Barwon Heads Alliance recommended that the lagoon should be protected by a geoheritage conservation zone of low intensity land use.

It stated that: "The key elements of this site are relatively inconspicuous, low relief landforms that preserve the materials and the geometry of the earlier sea level landscapes.

Research into geoscience features is an ongoing activity as new techniques of analysis and particularly for methods of mapping and displaying geomorphology and dating materials and landforming events become available.

The opportunity for further research and monitoring of the processes that formed Murtnaghurt Lagoon would be greatly compromised by extending urban or other high intensity built developments enclosing and adjacent to the site.