To address some challenging biological and environmental problems, scientists at the Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL) have been pairing scientific capabilities at their home institution with the bright, tunable energy x-rays and high-resolution instruments at several national synchrotron user facilities. Synchrotron techniques can help answer a variety questions, and two examples featuring synchrotron-based structural and chemical imaging in bio/geochemical systems will be presented. In the first example, x-ray fluorescence spectromicroscopy and microtomography were used to visualize and better understand phosphorous uptake in poplar trees. Endophyte-promoted phosphorous uptake was seen inside poplar roots, where the fixated phosphorous appeared to be in the form of an organic phosphate. Analysis of the tomography data showing increased root mass for the plants inoculated with the endophytes supported the picture of increased nutrient uptake in those plants. These results along with in-house proteomics characterization point to the biological relevance of the symbiosis between endophytes and the host plant. In the second example, scanning transmission x-ray microscopy (STXM) combined with x-ray absorption near edge structure (XANES) helped us investigate soil mineral – soil organic matter (SOM) interactions in an alkaline soil from Washington state. Ca mineral–organic associations were found to be predominant which may play a critical role in the stabilization/degradation of SOM and mineral. Micro- and nanoscale characterization of the chemical state of both Ca from the mineral and C from the organic matter are crucial for understanding such stabilization mechanisms as well as soil nutrient dynamics.