Proper water management of effluent/rainwater run-off and waste water would go along way.
In my home city, some councils are now wising up, and putting in wetlands to catch excess rain water and filter pollutants. The issue is room. There just isnt any. Adelaide City coucil is considering a huge allotment of space for wetlands, I cant wait.
Re-Veg in and around major water courses is also another promising method to reduce sediments, nutrient levels and pollutants.
I cant recall the name of the stuff, but some cities all over the world are now using a product like the stuff you see on the floors of McDonalds playgrounds to let water re-charge into the ground, rather than being guided off into drains, and eventually into the ocean.
Im not familiar with the actions being undertaken to prevent such sedimentation and nutrients entering the GBR from local sources. Because the GBR is now classed as a world heritage site, Im not 100% sure our Government is forced to look after it. (Although, im sure we do, as its a huge resource). You might find more info here:
Great Barrier Reef (GBR) Marine Park Authrority