North Queensland researchers are using satellite imagery to protect the Great Barrier Reef from polluted land run-off.

Scientists at James Cook Univeristy analyse images from space provided by NASA to assess what impact heavy rain, cyclones and pollutants have on the World Heritage listed reef and seagrass beds.

TropWATER project leader Dr Michelle Devlin said researchers identify river flood plumes where pollutants are running off into the Coral Sea and then use algorithms developed by NASA and CSIRO to determine the amount of suspended sediment or phytoplankton is in the water. 

Dr Devlin said the images are cheaper and less labour intensive than traditional methods of monitoring flood plumes which require scientists to use submerged data loggers, or boats and helicopters to gather water samples.

"It's a way of adding to your data," she said. 

"We still do all the in-situ sampling because you need to do that but we can now fill in the gaps between samples. 

"It's an inexpensive way to provide additional data and increase the complexity of the data. 

"Obviously it just takes additional time to asses but it's a fantastic tool." 

TropWATER's Dr Caroline Petus is the lead author of two studies that use the satellite images to monitor run-off.

The studies are a step towards developing river plume risk maps for Great Barrier Reef seagrass and coral ecosystems, Dr Petus said.

"Combined with ecological and in-situ water quality data, these maps will help our understanding of the resilience of these ecosystems to water quality changes," she said. 

"In the near future they should help us predict ecosystems' health changes associated with human activities or climate change."

Seagrass expert, Dr Michael Rasheed, said the information will help researchers understand the impact of flood plumes.

"It is often difficult to determine whether declines in seagrass beds are due to polluted river run-off or coastal development such as dredging around a port. This new tool will allow us to better understand which activities are driving declines," Dr Rasheed said.

Researchers hope the new monitoring techniques help prioritise how money is spent to better protect the Great Barrier Reef in the future.