The Cook Islands director of environment says there are ongoing concerns about pollution levels in the lagoons.
New tests are being conducted on Takitimu after people complained of irritants affecting their health in 2004.
The Takitimu lagoon in Rarotonga is thought to fall short of acceptable World Health Organisation standards.
Vaitoti Tupa says an NZAid-funded environmental impact assessment programme is helping them with further research on a number of lagoons.
He says together with the marine department, it's hoped the programme will pinpoint determining factors.
"Pig farms, tourist accommodation and we're also looking at residential areas in the foreshore. So these are the main issues we need to identify and see how we can tackle these issues to minimise concern."
Mr Tupa says NZAid is contributing more than 65,000 US dollars towards the three-year programme.