Limits will be set for how much run-off farmers, miners and sewer operators can dump into the 500,000-year-old reef under new minimum standards.

It will mean a reduction to the amount of nutrient, sediment and pesticide run-off into water catchments stretching up and down the Queensland coast.

A handful of government MPs won a small reprieve for industry, ensuring they will be spared further changes for five years.

They argued both the reef and the state's agriculture sector were important to Queensland, but that balancing them against one another was a priority.

During parliamentary debate, some MPs raised concerns about the unintended consequences for farmers who have already voluntarily scaled back their run-off, and who are still gripped by or recovering from drought and floods.

Runoff reduction schemes have been voluntary for the past decade, but it hasn't led to a significant decrease in runoff.

"Questions are being asked why it is only the farming community being targeted," independent Noosa MP Sandy Bolton said

"The scientific consensus report concluded it was a combination including coastal developments such as housing as well as dirt roads, gullies and erosion on state owned lands.

"There is also discontent in that we have been repeatedly told that the greatest challenge to the reef is extreme weather events and warming of waters."

Ms Bolton said Queensland' role as the world's third-largest fossil fuels exporter should not be overlooked.

"If we subscribe to the beliefs surrounding the contributors to climate change, we need to be consistent in our efforts to avoid being labelled as hypocrites."

Earlier this year, lobbyist AgForce deleted a trove of data, claiming the government would use it to fine farmers for non-compliance in future.

That claim was dismissed by Environment Minister Leeanne Enoch, who said the bill did not give government power to demand that sort of data.

Australian Associated Press