During the Pleistocene era tectonic uplift caused the level of the Gambier Embayment to rise. This uplift, and numerous variations in sea level, super^Anotimposed a series of sub-parallel calcareous sandstone dunes over the Gambier Limestone. Erosion of the Gambier Limestone during this period produced the karst features, including caves, cenotes and surface karren, of the lower south east.
Today water from the south east coastal plains drains underground through the Gambier Limestone in a south to south easterly direction towards the coastal discharge zone, between Port MacDonnell and the Glenelg River. Swamps and lagoons occur in those areas where the water table intersects the surface, or where surface water is restricted from draining to the sea by a coastal dune barrier.
The permanent freshwater ponds within the Piccaninnie Ponds Conservation Park are bounded by a stable coastal sand dune system to the south and a low calcarenite dune range to the north. The pond water levels are often above the water table level. Organic material trapped behind the calcarenite dunes prevents the water draining through the limestone. The deep-water section of the Ponds system was formed as dissolution of the limestone along a fault line formed caverns and tunnels.