Abstract The subsurface provides multiple resources, the exploitation of which has a lasting impact on future potential provision. Establishing sustainability in terms of fundamental principles, and fitting these principles into a practical framework, is an ongoing endeavour focused mainly on surface activities. The principles of ecological economics lead to six challenges that summarize the current limitations of implementing science-based sustainable management of geological resources in the medium to deep subsurface: integrating value pluralism, defining sustainable scale, evaluating interferences in the subsurface, guaranteeing environmental justice, optimizing environmental and economic efficiency and handling uncertainties. Assessing and managing geological reservoirs is particularly challenging because of slow resource regeneration, complex spatial and temporal interactions, concealment and naturally dictated opportunities. In answer to the challenges, visions are proposed that outline how an indicator framework is needed for guidance, how indicators require reservoir models with extended spatial and temporal scope, how differences in social values in relation to the environment are to be considered and how real option games combined with life cycle assessment can be used for optimizing efficiency. These individual solutions relate to different facets of the same problem, and can be integrated into one overarching solution that takes the form of dynamic multi-criteria decision analysis.