Over the past three years, scientists have been closely monitoring the condition of Lakes Hayes, Johnson, Onslow, Wakatipu and Wanaka.
They were monitoring the trophic levels of the lakes, which dictated their productivity or biological growth, water quality scientist Rachel Ozanne told the council's environmental science committee in a report this week.
"These values help determine the baseline general health of the lake and can be used to detect any further changes."
Environmental information and science director John Threlfall said the study provided a baseline so a similar study could be undertaken in 10 or 20 years to see whether there had been changes.
Ms Ozanne said the results showed lakes Hayes, Johnson and Onslow had high levels of nutrients, while lakes Wakatipu and Wanaka had low nutrient content and were very stable.
Low productivity, nutrient-poor lakes usually had clear water, and moderately productive or nutrient-rich lakes with high levels of productivity were often "murky and green because of algal growth".
Algal concentrations were low in lakes Wanaka and Wakatipu, but there was a trend of increasing biomass, she said.
Further monitoring of lakes Hayes and Johnson were planned in the summer, with the council initiating a collaboration with researchers from the University of Otago to provide additional analysis of factors causing the algal blooms in Lake Hayes.
