Responding to the threat of climate change, conserving freshwater ecosystems and securing adequate energy and water supplies are among the greatest challenges facing modern societies. Yet recognition of the interdependencies between climate, energy and water policy—with resulting synergies and trade-offs—remains limited, leaving societies and governments alike vulnerable to the dangers of conflicted or unintended policy outcomes from sectoral decisions. In this paper, we analyse current Australian climate, energy and water policies to identify the risks of perverse outcomes between the three policy sectors. In doing so we categorise the conflicts and synergies between particular energy generation, carbon sequestration and water supply policies to improve understandings of the challenges facing decision makers in Australia and internationally. Four types of interventions are identified that would enable integration and optimisation of policies, namely: better cross-sectoral knowledge to inform decisions; the identification of technologies with co-benefits; markets with broader cross-sectoral participation (including linking water and carbon markets); and better-integrated governance institutions.