The protection of ecosystems associated with groundwater, and thus potentially vulnerable to groundwater exploitation, is only now being recognised as an important aspect of water management. Although there has been a gradual increase in scientific understanding of the links between groundwater availability and ecosystem health, a significant challenge remains in the development and implementation of policy that adequately addresses the protection of groundwater-dependent ecosystems. There is no single right way to solve the problem of protecting groundwater-dependent ecosystems, while still allowing the use of groundwater to support social and economic development, poverty alleviation and improved food and water security. This paper provides a global perspective in examining the potential impacts of the lack of policy, or poor implementation of policy, related to groundwater-dependent ecosystems, and discusses emerging approaches in this field. The following two important factors are considered in the paper: first, the difficulty of managing typically local- and regional-scale problems associated with groundwater exploitation, by using national-scale policy interventions and regulation; second, the need to shorten the cycle from science to policy and regulation, and thence to management activities on the ground, in order to encourage policy shifts in the short to medium term that better reflect the available scientific knowledge of groundwater-dependent ecosystems.