Integrated water resources management offers an ideal platform for addressing the goals of freshwater conservation and climate change adaptation. Environmental flow assessment and systematic conservation planning have evolved separately in respective aquatic and terrestrial realms, and both are central to freshwater conservation and can inform integrated water resources management. Integrating these two approaches is mutually beneficial. Environmental flow assessment considers dynamic flow regimes, measuring social, economic and ecological costs of development scenarios. Conservation planning systematically produces different conservation scenarios that can be used in assessing these costs. Integration also presents opportunities to examine impacts of climate change on conservation of freshwater ecosystems. We review progress in environmental flow assessment and freshwater conservation planning, exploring the mutual benefits of integration and potential ways that this can be achieved. Integration can be accomplished by using freshwater conservation planning outputs to develop conservation scenarios for assessment against different scenarios, and by assessing the extent to which each scenario achieves conservation targets. New tools that maximise complementarity by achieving conservation and flow targets simultaneously should also be developed.