Worldwide, irrigation development has affected pre-existing natural habitats and created novel aquatic habitats, and future changes in management will continue to influence flood-dependent vegetation and fauna. Irrigated agriculture has had a profound influence on native biodiversity in the Riverina region of temperate Australia. Current irrigation practices provide large amounts of water to the landscape in the form of constructed wetland habitats: irrigation channels, impoundments and flooded crop-growing areas. Flooded rice bays support many species of native wetland plants, and 12 of the 14 species of frog recorded in the region. All constructed habitats provide a food resource for waterbirds, but not breeding habitat. While a species of tortoise benefits from the provision of constructed habitats, terrestrial reptiles and mammals are most abundant in remaining native vegetation. The climate is predicted to become increasingly hot and dry, with a reduced and more variable supply of irrigation water, thus placing increasing stress on farming and on natural ecosystems. The predicted reduction of constructed aquatic habitats may affect the native species using them, but may not have a major adverse impact on biodiversity regionally because the species recorded in constructed habitats tend be abundant and widespread, and such species also occur in natural wetland habitats. Sensitive species that depend on native vegetation persisting in reasonable amounts and in good condition are at greater risk. In the Riverina, the remaining native vegetation should be managed to protect and improve its condition, including appropriate managed inundation events for flood-dependent communities. The landscape should be managed to provide the best context for the function and health of existing vegetation including moderating the effects of soil disturbance, fertilizers and herbicides. The impacts of changed irrigation practices should be mitigated through managed flooding of remnant vegetation. In countries with more evolved, traditional rice-growing systems than the Riverina, there will be greater emphasis on biodiversity coexistence with cultivation. Nonetheless, in all settings there is value in jointly considering the role of both natural and constructed habitats in biodiversity research and conservation.