This research is an integrated project which uses physical (geophysical and hydrologic) and innovative geophysical imaging and microbial characterization methods to identify key scales of physical heterogeneities that affect bioremediation. In the this effort data from controlled laboratory and in situ experiments at the Idaho National Engineering and Environmental (INEEL) Test Area North (TAN) site were used to determine the dominant physical characteristics (lithologic, structural, and hydrologic) that can be imaged in situ and correlated with flow and transport properties. Emphasis was placed on identifying fundamental scales of variation of physical parameters that control transport behavior relative to subsurface microbial dynamics that could be used to develop a predictive model. A key hypothesis of the work was that nutrient flux and transport properties are key factors in controlling microbial dynamics, and that geophysical techniques could be used to identify the critical physical properties and scales controlling transport. This hypothesis was essentially validated. The goal was not only to develop and apply methods to monitor the spatial and temporal distribution of the bioremediation in fractured sites such as TAN, but also to develop methods applicable to a wider range of DOE sites. The outcome has been an improved understanding of the relationship between physical, chemical and microbial processes in heterogeneous environments, thus applicable to the design and monitoring of bioremediation strategies for a variety of environments. In this EMSP work we demonstrated that high resolution geophysical methods have considerable resolving power, especially when linked with modern advanced processing and interpretation. In terms of basic science, in addition to providing innovative methods for monitoring bioremediation, the work also provided a strong motivation for developing and extending high resolution geophysical methods.