So all existing licence users had to reapply for water rights. If they applied they got them. However if you did not then your licence lapsed. This has reduced the amount of water that was drawn from water supplies.
Licences are now traded on the market so if you want to increase the amount of water usage, you needed to buy one off someone who was selling. These were not transferable to different waterways. The amount of water that could be captured was limited to 10% of the water falling on a stakeholders land. Beyond that a water licence was again needed.
To this day there is considerable tension between irrigators and conservationists about what the right balance of water is for maintaining the environment while not decreasing food production.
The reason that Australia has a problem with water largely revolves around its scarcity. Because of this whole ecosystems have evolved to rely on seasonal variations of water like in the Snowy River, or cycles of drought and flood like the Murray Darling. Alterations to this can affect ecosystems and river health. In the worst case scenario the river may be classed as dead and the quality of the water decline to the point where it is unusable by all.