Refuges are important to the survival and persistence of aquatic organisms in drier landscapes and are particularly important during periods of seasonal or supra-seasonal drought. Natural instream refuges are primarily groundwater dependent, particularly those with medium to long-term persistence. The effective and sustainable management of important aquatic refuge habitat in groundwater dependent ecosystems (GDEs) in Victoria requires knowledge of their distribution, condition and environmental values. Current knowledge on tributary GDEs in Victoria is variable and generally poor, particularly those in unregulated streams in mid to upland areas of catchments. Improved knowledge of these aquatic refuges across the landscape is critical to inform effective management to improve the resistance and resilience of important aquatic populations, species, and ecological communities, particularly under future climate change scenarios. We investigated whether available remote sensing imagery/coarse spatial data could be used to predict the location of riverine GDEs at the local scale (subcatchment/tributary) in unregulated systems, and developed a rapid methodology, as a first step, for the identification of GDEs potentially important as refuges for drought sensitive aquatic fauna.