The rivers of south-eastern Australia flow within a complex meander tract (Coonambidgal Formation) formed by phases of Quaternary stream activity. Pumping tests, hydrochemistry and groundwater monitoring of the Campaspe, Loddon and Murray River Valleys show that for significant parts of their courses, the rivers and their associated strip aquifers form a single integrated hydraulic unit perched above and disconnected from the regional water table by an underlying aquitard developed at the top of a varyingly thick and temporally dynamic vadose zone. Loss to the regional aquifer is not restricted to the riverbed but covers the entire width of the Coonambidgal Formation aquifer, which is one or two orders of magnitude greater. River-bed flux is not a measure of net river loss. Through diffusion and dispersion from the overlying saturated zone, aquitard enhancement or development is augmented by chemical processes active towards the top of the vadose zone. Unlike river-bed clogging, chemical clogging of aquifers is progressive and permanent. Post-European instability in the studied groundwater systems has seen catchment wide groundwater rises of up to 0.25 m/y. or 25 metre over the last century. Under the pre-existing norm of deeper water tables, disconnected streams would have been more numerous with the present aquitards being a legacy of that regime.