Environment Minister Peter Garrett said the funds included $4.5 million for monitoring water quality in rivers and wetlands, monitoring and encouraging improvements in land management and land condition throughout the catchment, and looking at marine water quality and ecosystem health.

"A further $2 million will go to trialling new technologies that improve water quality in the catchment and for developing and applying new water quality monitoring techniques for nutrients, chemicals and sediments," Mr Garrett said.

"Partnerships with traditional owners will see up to $1 million over this financial year go towards improving sea country management, helping to conserve such species as turtle and dugong."

Agriculture Minister Tony Burke said funds would also be spent in the reef catchment range improving nutrient and chemical application on farms, using controlled traffic farming and machinery conversions, fencing off waterways, and improving management and community understanding of habitats on the coast and in the waters of the reef lagoon.

"We’ve asked the regional Natural Resource Management groups, in partnership with agricultural industry groups and the World Wildlife Fund in the Reef catchment, to come up with projects for the current financial year based on an indicative budget for their region," Mr Burke said.

"We’ll be considering these projects in the next month."

The funding will benefit the Mackay Whitsunday region, Terrain region, Burdekin Dry Tropics region, Fitzroy Basin region, Burnett region and Cape York region.