Understanding the fate of metals and metalloids in soils is of fundamental importance in the development and evaluation of effective remediation and sequestration strategies. In addition to mineral surfaces, bacteria and the extracellular material associated with them play a key role in determining a contaminant's speciation and thus its mobility in the environment. Additionally, the metabolism and surface properties of bacteria can be quite different depending upon whether the bacteria exhibit a planktonic (free-floating) or biofilm (surface adhered) habit. The microenvironment at and adjacent to actively metabolizing cells also can be significantly different from the bulk environment. Thus, to understand the microscopic physical, geological, chemical, and biological interfaces that determine a contaminant's macroscopic fate, the spatial distribution and chemical speciation of contaminants and elements that are key to biogeochemical processes must be characterized at micron and submicron length scales. Hard X-ray absorption spectroscopy and microimaging are powerful techniques for the element-specific investigation of chemical reactions in complex environmental samples at the needed micron and submicron resolution. An important advantage of these techniques results from the large penetration depth of hard X-rays in water. This advantage minimizes the requirements for sample preparation and allows the detailed study of hydrated samples. The objectives of the studies to be presented are (1) to determine the spatial distribution, concentration, and chemical speciation of metals and metalloids at, in, and near bacteria and bacteria-mineral interfaces, (2) to use this information to identify the metabolic state of the microbes, and (3) to identify the interactions occurring near these interfaces among the metals, mineral surfaces, and bacteria under a variety of conditions. We have used X-ray Absorption Fine Structure (XAFS) spectroscopy to identify the chemical speciation of uranium in a number of biogeochemical systems. We also have used X-ray fluorescence microscopy and microspectroscopy to investigate the spatial distribution of elements and their chemical speciation in a number of different biogeochemical environments. Finally, we have used X-ray microtomography to investigate porosity in virgin prairie and agricultural soil aggregates. These results and a discussion of the use of these techniques for identifying metabolic states of individual microbes within communities and the chemical speciation of metal contaminants at the mineral-microbe interface will be presented.