Most conservation efforts in aquatic ecosystems focus on surface waters. This is understandable given their public visibility, accessibility and, in many parts of the world, stark evidence of their vulnerability to human impact. On the other hand, programmes to protect and conserve groundwaters, and the ecosystems that rely wholly or partially on access to groundwater, are far less common. Contaminated groundwater is less obvious to the public than a blue-green algal bloom or the floating corpses from a fish kill. Increasingly, as surface waters become polluted, groundwater resource use is intensifying in many parts of the world, often mining resources faster than they are replenished (Danielopol et al., 2003). We are realizing that groundwater is not an inert, lifeless resource, but instead can harbour considerable biodiversity of invertebrates and microbes (Marmonier et al., 1993; Danielopol et al., 2000) whose activities provide crucial ecosystem services in nutrient transformation and biological filtration (Boulton, 2000; Hancock, 2002). There are growing numbers of examples of catastrophic crashes in groundwater ecosystems due to saline intrusion (Ergil, 2000) and over-extraction (Kromm and White, 1992) while in other areas, contaminants such as heavy metals are rendering groundwater toxic to millions of humans (Nickson et al., 1998; Sengupta et al., 2001). The key issue is one of public and political education about the conservation values, ecosystem services, and subsurface-surface linkages of groundwaters. While knowledge gaps still exist, I suggest that we know enough to be able to advise policy-makers and governments about the benefits of conservation of groundwaters and their dependent biota. Recent editorials in this journal have highlighted the ecological significance of hydrologic connectivity (Pringle, 2003) and restoration science at large scales (Ormerod, 2004). My contribution builds on these to provoke research and debate about conservation of groundwaters and their linkages at suitable scales, potentially requiring restoration of groundwater quality and water regime to benefit significant groundwater-dependent ecosystems (GDEs).