The area is normally known for wildlife like Australasian crested grebes and secretive wetland birds like bitterns, as well as recreational fishing, boating, and windsurfing.
Martin said neither district nor regional councils are doing enough to protect fresh water.
"There are standards in place and monitoring is occurring, but after 15 years of failing to meet their own standards the regional council has not taken the actions necessary to actually stop intensification and the extensive use of fertilisers.
"They need to take action now. We could lose these incredible natural lakes and essential habitats. I worry it may already be too late."