Ephemeral deflation basin lakes are widespread throughout arid and semiarid regions of the Murray–Darling Basin in Australia. Although they are diverse, productive habitats, the water resources development has generally caused significant declines in their ecological condition. Managers are currently trying to protect or restore these systems, however, without an adequate theoretical framework on which to base management decisions. This is because the existing conceptual models provide little insight into the effects of any component of the flow regime except flooding. This paper reviews the effects of flooding and drying on lakes, using the information and conclusions therein to propose a conceptual model that identifies five stages in the flooding and drying cycle. This conceptual model incorporates elements of the Flood Pulse Concept, Trophic Cascade models and the Geomorphic–Trophic model, as they apply to these highly variable water systems.