The German Continental Deep Drilling Program comprising a pilot borehole down to 4000 m and a main borehole down to 9101 m in southeast Germany (KTB) is continuing to provide a unique opportunity for the identification of important factors and processes in deep-seated fluid and energy transfer. In situ stress conditions significantly impact flow, transport and exchange characteristics of fracture networks that dominate the permeability of crystalline reservoir rocks. In this paper, several scales of information are combined to present a fully three-dimensional hydraulic finite element model of the principal KTB fault zones, and linked to a geomechanical model describing the alteration of the hydraulic parameters with stress changes caused by fluid extraction. The concept of geomechanical facies is introduced to define and characterize architectural elements in the subsurface system. Evaluation of a long-term pump test in the KTB pilot hole, June 2002–July 2003, coupled with a geomechanical model gives an insight into some of the elastic and nonelastic processes controlling hydraulic transport in the basement rocks. Trends in the decline of the permeability and the degree of storage in the system could only partially be explained by elastic processes, clearly indicating the importance of nonelastic processes. A number of inelastic processes are suggested as areas for further research.