"Water quality can be impacted by things such as climatic conditions and rainfall," he said.
"Although many lakes reached their [targets] last year, this year's were impacted by a warm, settled summer ... This was particularly true for lakes Rotorua and Rotoehu, which saw a decline in water quality.
"To complement the Index we have a number of different scientific monitoring systems that measure the environmental quality of each lake."
He said these systems include cyanobacterial (algae) monitoring, live monitoring buoys which collect data on lake water quality 24 hours a day on some of the lakes, native and introduced fish monitoring, as well as water chemistry testing.
Improved water quality was recorded in lakes Okaro, Rerewhakaaitu and Tikitapu.
Previously improving levels in lakes Rotorua, Rotoehu and Rotoiti declined this year.
Stable water quality was recorded in lakes Okataina, Okareka, Rotoma and Rotomahana, while further long-term deterioration was recorded in lakes Tarawera and Rotokakahi.
Mr Bruere said this year's results reinforced the importance of long-term thinking for improving water quality.
"There has been significant work into lakes restoration over recent years with the long-term trend for many lakes improving, as indicated by some of our lakes reaching their targets last year," he said.
"The decline for some lakes, notwithstanding climatic variations, highlights the importance of long-term sustainable solutions to protect water quality."
He said it reinforced the fact there was "no quick or easy fix".
Te Arawa Lakes Trust chairman Sir Toby Curtis said progress had been made but there was still a lot to be learned.
"We're still learning about nutrient run-off and we think we've got it worked out but then the kind of weather that occurs can play havoc.
"All of the people in the area are conscious they have a part to play. We have to acknowledge that some are maybe coming on board at the expense of their own quality of life, in terms of income they're making from the land. That is something we cannot ignore."