Last summer's warm weather had a bad effect on some of the Rotorua-Te Arawa lakes, with water quality declining.
Bay of Plenty Regional Council's latest study said there was an improvement in just three of the 12 lakes during the past year.
Lakes operations manager Andy Bruere said the hot summer weather caused lakes such as Rotorua, Rotoiti and Rotoehu to become stagnant, allowing more algae to grow.
"They stratify because of the difference in temperature and if that releases nutrient then it allows more algae to grow in the lake, which is part of the measurement that gives us the water quality for the lake."
The results were disappointing considering there had been significant work into lakes restoration over recent years, Mr Bruere said.
Water quality was judged by measuring total nitrogen, phosphorous, water clarity and chlorophyll-a.