For the first time, scientists have successfully produced digital maps for the entire Great Barrier Reef off Queensland.

Until now, nearly half of the shallow water reef areas had not been mapped using modern digital surveys.

Australian and German scientists have now produced 3D water depth maps covering the 350,000 square kilometres of the world heritage area.

James Cook University's Dr Robin Beaman says the maps provide a complete picture of the reef ecosystem.

"You can see the shape of individual reefs, you can see where the lagoons are, where the reef flats are," Dr Beaman said.

"Prior to this data many of the reefs ... there was very little detail over them, they would just show up as a flat bump on the sea floor, well this is not the case now, the data allows us to detail that, it's really unprecedented."

Dr Beaman says the maps could help researchers better understand threats to the reef such as crown of thorns starfish.

"If you can understand how larvae interacts and flows in and around coral reefs, you stand a better chance of understanding where that larvae travels to and of course predicting where the next outbreak goes," he said.