Groundwater is a vital water supply worldwide for people and nature. However, species and ecosystems that depend on groundwater for some or all of their water needs, known as groundwater-dependent ecosystems (GDEs), are increasingly becoming threatened worldwide due to growing human water demands. Over the past two decades, the protection and management of GDEs have been incorporated into several water management policy initiatives worldwide including jurisdictions within Australia, the European Union, South Africa, and the United States. Among these, Australia has implemented the most comprehensive framework to manage and protect GDEs through its water policy initiatives. Using a science-based approach, Australia has made good progress at reducing uncertainty when selecting management thresholds for GDEs in their water management plans. This has been achieved by incorporating appropriate metrics for GDEs into water monitoring programs so that information gathered over time can inform management decisions. This adaptive management approach is also accompanied by the application of the “Precautionary Principle” in cases where insufficient information on GDEs exist. Additionally, the integration of risk assessment into Australia’s approach has enabled water managers to prioritize the most valuable and vulnerable ecologic assets necessary to manage GDEs under Australia’s national sustainable water management legislation. The purpose of this paper is to: (1) compare existing global policy initiatives for the protection and management of GDEs; (2) synthesize Australia’s adaptive management approach of GDEs in their state water plans; and (3) highlight opportunities and challenges of applying Australia’s approach for managing GDEs under other water management policies worldwide.