Conflict over water allocations and the need to adapt to climate change in Australia’s Murray-Darling Basin has resulted in decision makers choosing engineering interventions to use water more efficiently for wetlands conservation. We review a range of policy and infrastructure adaptation measures implemented in the Basin by governments. The water supply and demand “environmental works and measures” adopted in the Coorong and Lower Lakes region, as well as along the River Murray, are assessed and compared with the opportunity costs for ecosystem-based adaptation. The results suggest that risks of disruption to ecological processes, desiccation of wetland areas and institutional failure with infrastructure-led adaptation measures are little appreciated. Further, ecosystem-based measures to maintain a more diverse range of ecological processes that would spread risk and conserve a more diverse range of biota have not been identified or adopted by governments. We conclude that as a primary adaptation to climate change environmental works and measures may represent overly-narrow or mal-adaptation that can reduce the resilience of wetland ecosystems.