Energy dispersive X-ray fluorescence (EDXRF) provides highly sensitive and precise spatial resolution of cation content in individual annual growth rings in trees. The sensitivity and precision have prompted successful applications to forensic dendrochemistry and the timing of environmental releases of contaminants. These applications have highlighted the need to distinguish dendrochemical effects of internal processes from environmental contamination. Calcium, potassium, and zinc are three marker cations that illustrate the influence of these processes. We found changes in cation chemistry in tree rings potentially due to biomineralization, development of cracks or checks, heartwood/sapwood differentiation, intra-annual processes, and compartmentalization of infection. Distinguishing internal from external processes that affect dendrochemistry will enhance the value of EDXRF for both physiological and forensic investigations.