Scientists will examine the health of 380 New Zealand lakes in a new project granted $12 million in government funding.
The study to be carried out by GNS Science and the Cawthron Institute will include analysis of sediment to detect why changes in the lakes are happening.
Programme leader and GNS scientist Marcus Vandergoes said while only 10 percent of the country's lakes would be analysed, that would be enough build a picture of all lakes.
Dr Vandergoes said some lakes had changed due to natural nutrients in the catchments, and others through human activity.
"There is increasing pressure to increase national water quality from all different regions," he said.
"It's important to have this informed benchmark of a natural state of these lakes and understand the features that may be driving changes in them."
Dr Vandergoes said the project had a lot of local government and iwi support.