It is also the main contributor to outbreaks of coral-eating crown-of-thorns starfish because the nutrients in fertilisers cause algae outbreaks that feed the starfish.
Sugarcane farmers in far north Queensland will be able to use a mobile app developed by the CSIRO,which will help them manage fertiliser use and help reduce nitrogen run-off on to the reef.
The free app,launched this week,shows data on nitrate concentrations from high-frequency automatic sensors deployed in selected coastal catchments.
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The information is fed directly to the app allowing growers to monitor the concentration of nitrogen in local waterways in real-time.
Scientists hope with easy access to water levels,farmers will be able to better manage the connection between farming in the catchment and water quality.
"Sugarcane growers told us they wanted quick and easy access to water quality information,so they could find out what's going on with their crops and make better decisions,"CSIRO agricultural scientist and project leader Dr Peter Thorburn said.