On the rare occasions that Lake Hindmarsh overflows, water flows via Outlet Creek to Lake Albacutya. In most years the flow of the river does not reach those terminal lakes, and the watercourse itself contracts into a series of pools.
The passage describes a natural phenomenon where water from Lake Hindmarsh flows to Lake Albacutya through Outlet Creek in specific circumstances.  In most years, however, the flow is insufficient to reach these destinations, resulting in the river's contraction into a series of pools.