In this essay, “deep hydrogeology” is somewhat arbitrarily defined as hydrogeology in the subsurface deeper than 1 km, below which the effect of residual permeability at high stresses becomes evident (Neuzil 2003; Rutqvist and Stephansson 2003; Liu et al. 2009). Studies have shown that meteoric fluids are present in the earth’s crust from land surface to at least a depth of 10–15 km (Kozlowsky 1987; Taylor Jr 1990; Zharikov et al. 2003; Ge et al. 2003). At such depths, interaction with surface water and surface events over time periods of 100 or 1,000 years may be minimal, except in areas of very deep mining activities or where deep convection is enhanced by active magmatism. Deep drilling to several kilometers in depth is often done for petroleum and geothermal reservoir exploration and exploitation. The focus of such activities is reservoir identification, capacity evaluation, and fluid and heat extractability. However, it is largely an open area of research to understand the state, structure and evolution of deep hydrogeology over time scales of tens of thousands of years or more, especially in areas lacking petroleum and geothermal resources. Interest in attaining such an understanding has emerged from the need for long-term predictions related to nuclear waste disposal and from recognition of the role that hydrogeology may play in seismicity, orogenesis and various geological processes, as well as in global fluid and chemical cycles. A number of wide-ranging questions may be asked regarding deep hydrogeology, several of which are as follows: What are the current and past states of fluid pressure, temperature and chemical composition in deep formations? How does fluid transport mass and heat? What are the fluid sources and driving mechanisms? What are the magnitude and distribution of porosity and permeability? What are the occurrence and characteristics of large-scale flow, including thermally and chemically driven convection systems? What is the nature of local anomalous fluid pressures and what are their implications? The purpose of this essay is to discuss key issues and research needs in deep hydrogeology. It is based on a workshop on the subject held at Uppsala University in Sweden, with participants from 11 countries, including the USA, Russia, Japan and a number of European countries (Tsang et al. 2012). The following discussion will be divided into sections on permeability structures, driving forces, coupled processes, borehole testing and data analysis, followed by a few concluding remarks.