Water is the basis of all life on Earth but groundwater (the water stored beneath the Earth’s surface) is often ‘out of sight and out of mind’, despite its importance as a permanent source of water in otherwise dry landscapes. Groundwater supports ecosystems and biodiversity and plays an important role in culture and connection to country for Indigenous people. Access to freshwater for drinking is vital for the existence of many inland Australian towns and remote communities. This water is also an essential resource for many industries including agriculture, horticulture and mining. These underground reservoirs of water can act as a critical buffer for freshwater habitats in regions where future rainfall is predicted to decline with global warming. Groundwater-dependent systems are sustained by aquifers that are recharged by rain that has fallen either relatively recent or in the more distant past, or a mixture of both. Isotope hydrology is a useful tool for determining the relative contribution of old and new water sources (rainfall). Environmental DNA (eDNA) can be used to characterise the water quality and biota of both subterranean and aquatic groundwater dependent ecosystems. Combining these approaches with the collection of groundwater samples by citizen scientists is now being used to obtain the information needed to understand and manage groundwater in the wet/dry tropics and arid regions of northern Australia. The remoteness and vastness of this region means that community-based data collection and knowledge sharing may be the only way to support groundwater management and the conservation of groundwater dependent ecosystems across such large spatial scales.