Joe, actually they say they have no responsiblity below the high TIDE mark. Which is true, the ocean and tidal rivers are the state governments responsibility. Bligh is deliberately muddying the waters here if you excuse the pun.
If you think about it, no contamination of thsi nature can come from within the sea itself so provided councils monitor thier treatment plant outputs into the river (which they do, very rigerously) then any issues would be picked up very quickly at the source.
In a large flood event when sewerage plants cannot contain the flows, and in many cases are under water, then testing outflows becomes irrelevent. There are so many potential sources of contamination that cannot be controlled you can only assume that the water is contaminated until the plants are brought back on line.
As for regular testing of the lower brisbane river and bay, it is a state responsiblity. Non tidal creeks and inland rivers should be monitored by councils and enforced by the EPA.
I do agree with you that regular monitoring is sensible and should be done by the responsible entity. Most unexplainable contamination would probably come from burst/blocked/leaking pipes, not the plants themselves which operate under strict conditions.