More than half of 124 New Zealand lakes surveyed have either poor or very poor water quality.
The results are contained in a national summary compiled for the first time by Land, Air, Water Aotearoa (Lawa).
The organisation is a collaboration between councils, science and government agencies.
The summary revealed the poor condition of many of New Zealand's lowland lakes, but also the "spectacular quality" of some upland water bodies.
Cawthron Institute freshwater scientist Roger Young was part of the science team behind the summary. He said the results were concerning.
"We presented analysis based on the Trophic Level Index (TLI) because this index gives us an idea of how nutrient enriched a lake is," Dr Young said.
Nutrient overload can lead to phytoplankton growth, reduced clarity, and toxic algae blooms.
Dr Young said the scores showed the condition of fewer than one-in-five lakes could be categorised as either very good or good, whereas more than half were nutrient-enriched and therefore categorised as either poor or very poor.
"Most of the very poor condition lakes are lowland and most of the very good lakes are found at higher altitudes.
"This makes sense as most human activity occurs at lower altitude, and upland lakes are often surrounded by conservation land."
Lakes are monitored for a range of water quality (chemical-physical and bacterial) and ecological indicators by regional and unitary councils.
Monitored sites with the best data records in New Zealand were often located in areas more impacted by human activities, had the greatest social and cultural value, or where changes in perceived water quality had resulted in the implementation of monitoring programs.
Waikato Regional Council freshwater scientist Dr Deniz Ozkundakci said the study had given them a much better understanding of where the problems existed.
"We have now a much better understanding of where some of the problems exist, and where water quality is poor.
"It's probably also worth noting that some of those lakes will respond very, very slowly to interventions."
Water quality can be improved through a combination of community-based actions, effective policies, and implementation of restoration methods.
"Across New Zealand, there's some good work going on to support and improve our lakes, but it's important to understand that lakes can respond very slowly to restoration and management efforts.
"Protection of the most pristine lakes in New Zealand is of utmost importance," Dr Ozkundakci said.