The changes will have an impact on the future management of the reef and its marine protected areas, researchers said.
"When we looked back at satellite data collected since 1985, we found evidence that most of the regions of the GBR are changing significantly, in terms of sea surface temperature -- especially in the southern part of the reef," lead study author Natalie Ban of Australia's Center of Excellence for Coral Reef Studies said.
"Risk of coral bleaching increases with higher water temperatures," she said. "Across the whole reef we found water temperatures increasing by an average of 0.2 of a degree over a quarter of a century -- but the increase was significantly more in some areas."
Changes of water temperatures in particular places along the reef are changing seasonal patterns, she said.
"In some areas summer is coming earlier and lasting longer; in others, both summers and winters are warmer than in the past. This all affects the sea life."
"We hope that our research will also prove valuable to countries of the [Pacific] Coral Triangle who are trying to manage the world's center of coral diversity through this challenging period," she said.
Australia is considered a world leader in marine reef science and in managing coral reefs, LiveScience reported.