The park has a relatively high average annual rainfall of 1170 mm most of which falls in autumn and winter. The annual rainfall varies considerably over a long period. Consequently the ground water levels and depth of permanent waterbodies range from very low, after a series of dry years, to very high, after successive wet seasons. In some years, the water table extends to the surface in much of the low-lying western parts of the park.
The freshwater systems of the park range from ephemeral sheet and stream surface flows to permanent and semi-permanent streams, swamps and waterholes which may be self-contained or a surface expression of extensive ground water resources. All are integral components of the natural systems of the park and support varied and dependant plant and animal communities. There are several perched lakes. Lake Windemere and Lake McKenzie, both of which are closed freshwater dune lakes, are the largest permanent waterbodies in the park. Both are characterised by considerable cyclical water level fluctuations in response to climatic variations within a period of several years.
The relatively undisturbed condition, and the variety of plant and animal communities present, make the freshwater bodies of the park a valuable conservation and scientific reference resource. Alteration to catchment drainage patterns in swamp and wet heath areas can change the structure and composition of the vegetation.