The ecology of the Hattah Lakes and surrounding floodplain is strongly influenced by flooding regimes of the River Murray. The system fills when there are high flows in the River Murray, and some lakes hold water for numerous years after floods recede. Regulation of the River Murray has significantly reduced the frequency and duration of small- to medium-sized natural floods in the Hattah Lakes system. Over time, this has degraded vegetation communities and reduced the diversity and abundance of animals that use the vegetation and wetlands for habitat and food.
The Hattah Lakes complex can be broadly divided into the southern Hattah Lakes, which contain permanent to semi- permanent wetlands, and the higher-elevation northern Hattah Lakes, which are mostly ephemeral wetlands.
The Messenger, Oateys and Cantala regulators allow water to flow between the River Murray and the Hattah Lakes. When flows in the River Murray are about 26,000 ML per day, water begins to flow through the Messenger regulator into Chalka Creek and through to the Hattah Lakes complex. A permanent pump station has also been constructed that can deliver up to 1,000 ML per day to Hattah Lakes through Chalka Creek. The regulators and pump station are used in combination with several small constructed levees to restore a beneficial pattern of flooding to the lakes.
Lake Kramen in the south-east of Hattah-Kulkyne National Park is disconnected from the main Hattah Lakes complex. The Hattah Lakes pump station can deliver up to 145 ML per day to Lake Kramen to restore flooding regimes.