Thank you for your question about the three levels of governance. The answer depends on the size and type of the water project.
In the Australian Constitution, water infrastructure and dams are not listed as federal government responsibilities, meaning states and territories have this responsibility. State governments may often give responsibility for the day to day management and delivery of water to residents, to local councils. As some water projects that are very big and the rivers involved may cross state boundaries, these projects may have to involve the federal government.
One such example is the Snowy Mountains Hydro-Electric Scheme. The Federal Parliament History Timeline has information on this (see Snowy Mountains Hydro-Electric Power Act 1949).