The soils of Yalgorup National Park originated from the sea. They are largely made up of calcareous material derived from sea shells and other marine organisms. These soils, deposited in a series of dune ridges parallel to today's shoreline, also illustrate past changes in sea level. As the polar ice caps grew during the last ice age (which began approximately 130,000 years ago), the sea level gradually fell, fluctuating as it did so. It reached its lowest point, 130 metres below its present level, about 18,000 years ago. It then rose after the ice age ended some 10,000 years ago, producing the shoreline we see today.

The dune systems within Yalgorup National Park are the result of these changes. The limestone rocks and soils that can be seen at the surface inland from the coast are derived from the older Spearwood system, which formed in the last 10,000 to 140,000 years. The Spearwood system is reflected by leached sands at the surface and creamy yellow to reddish-brown subsoils. The Spearwood beds also extend well offshore. Superimposed over the Spearwood system, for up to two kilometres from the beach, are the sand dunes of the Quindalup Dune System, which have been blown in from the sea or washed ashore over the last 10,000 years.

The lakes that characterise the park lie in the depressions between a series of coastal dunes within the Spearwood system. Reflecting this underlying structure, the ten lakes form three distinctive lines parallel to the coast. Lake Preston is extremely elongated and lies closest to the coast. The lakes behind the next ridge are far more broken, comprising (from north to south): Swan Pond, Duck Pond, Boundary Lake, Lake Pollard, Martins Tank Lake, Lake Yalgorup, Lake Hayward and Newnham Lake. Lake Clifton is the furthest from the coast and the nearest to the Old Coast Road. It too is extremely elongated.

The Yalgorup lake system is so significant for waterbirds that it is recognised under the international Ramsar Convention (named after the place where it was signed in Iran). The lakes provide important habitat for the international transequatorial waders that migrate from the northern hemisphere. These waders include the bar-tailed godwit, red-necked stint, greenshank, red knot, whimbrel and three species of sandpiper. Other waterbirds that use the lakes include the banded and black-winged stilts, red-necked avocet, hooded and red-capped plovers, Australian pelican and coot.

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