Resolving the distribution and speciation of metal(loid)s within biological environmental samples is essential for understanding bioavailability, trophic transfer, and environmental risk. We used synchrotron x‐ray microspectroscopy to analyze a range of samples that had been exposed to metal(loid) contamination. Microprobe x‐ray fluorescence elemental mapping (µSXRF) of decomposing rhizosphere microcosms consisting of Ni‐ and U‐contaminated soil planted with wheat (Triticum aestivum) showed the change in Ni and U distribution over a 27‐day period, with a progressive movement of U into decaying tissue. µSXRF maps showed the micrometer‐scale distribution of Ca, Mn, Fe, Ni, and U in roots of willow (Salix nigra L.) growing on a former radiological settling pond, with U located outside of the epidermis and Ni inside the cortex. X‐ray computed tomography (CMT) of woody tissue of this same affected willow showed that small points of high Ni fluorescence observed previously are actually a Ni‐rich substance contained within an individual xylem vessel. µSXRF and x‐ray absorption near‐edge spectroscopy (XANES) linked the elevated Se concentrations in sediments of a coal fly ash settling pond with oral deformities of bullfrog tadpoles (Rana catesbeiana). Se distribution was localized within the deformed mouthparts, and with an oxidation state of Se (−II) consistent with organo‐Se compounds, it suggests oral deformities are caused by incorporation of Se into proteins. The range of tissues analyzed in this study highlight the applicability of synchrotron X‐ray microspectroscopic techniques to biological tissues and the study of metal(loid) bioavailability. This paper was by special invitation as a contribution to a special issue of the journal entitled “Application of Spectroscopic Methods to Environmental Problems.” The special issue was organized by Professor Peter A. Tanner, Professor in the Department of Biology and Chemistry at City University of Hong Kong.