AFAIK not a lot of cotton farming going on in reef catchment areas. There is lots of sugar cane and bananas however. Also lots of deforestation for grazing. Plus major resource export ports (LNG, coal). Regardless, runoff remains a major topic and there is some progress being made in the space [1].

Regards the article. If you look to the report itself[2] you'll see that this isn't a "she'll be right" triumph of science over scare campaigns. Climate change sits at the top of a growing list of concerns. The summary specifically mentions increased frequency of both marine heatwaves (that lead to bleaching) and major destructive weather events like cyclones. The other serious concern is crown-of-thorns starfish (a sea star that eats coral) ... and while the jury may still be out on the cause of their outbreaks (overfishing of predators? excess nutrients? changing environment?), the effect of this single species on the broader ecosystem is beyond frightening to witness.

It's extremely difficult to have a meaningful conversation about the threats to the reef without getting into the weeds. The "scare" campaigns may be light on detail, glossing over (or ignoring) much of the important nuance, but (for the most part) they aren't wrong.

[1] https://www.gbrmpa.gov.au/our-work/threats-to-the-reef/decli... [2] https://www.aims.gov.au/monitoring-great-barrier-reef/gbr-co...