The national park was declared in 1921 and has been expanded significantly since, to protect 357,017 hectares (882,210 acres) of mallee, woodland, and heathland.

The current landforms took shape as the sea gradually retreated from 40,000 to 15,000 years ago, leaving a vast expanse of sandy sediment which formed into sand dunes as it dried.

Before European settlement, a network of ephemeral lakes in the area filled and emptied, on average, about every 20 years, typically remaining dry for about half that period.

More recently, agricultural irrigation and drainage projects in the surrounding areas have cut off a significant part of Wyperfeld's water supply.

Given sufficient rain in the catchment, the water flows further north into Wyperfeld itself, forming a series of smaller lakes, which support rich floral and faunal communities based around black box and river red gum.