Throughout the world, organic and inorganic substances leach into the subsurface as a result of human activities and accidents. There, the chemicals pose direct or indirect threats to the environment and to increasingly scarce drinking water resources. At many contaminated sites the subsurface is able to attenuate pollutants which, potentially, lowers the costs of remediation. Natural attenuation comprises a wide range of processes of which the microbiological component, which is responsible for intrinsic bioremediation, can decrease the mass and toxicity of the contaminants and is, therefore, the most important. Reliance on intrinsic bioremediation requires methods to monitor the process. The subject of this review is how knowledge of subsurface geology and hydrology, microbial ecology and degradation processes is used and can be used to monitor the potential and capacity for intrinsic bioremediation in the subsurface and to verify degradation in situ. As research on natural attenuation in the subsurface has been rather fragmented and limited and often allows only conclusions to be drawn of the site under investigation, we provide a concept based on Environmental Specimen Banking which will contribute to further understanding subsurface natural attenuation processes and will help to develop and implement new monitoring techniques.