Steller sea lion (Eumetopias jubatus) tissue mercury concentrations increasingly above thresholds of concern occur in regions of Alaska where lack of population recovery is noted. Selenium–monomethylmercury interactions may mitigate toxicosis but may also result in functional selenium deficiency, impacting essential selenium‐dependent processes. Physiologically driven differences in tissue concentrations (organotropism) of total mercury (THg), total selenium (TSe), and monomethylmercury (MeHg+) confound interpretation for various age cohorts. Archived tissues from Alaska Steller sea lions (2002–2016) were used to compare THg, MeHg+, and TSe across age cohorts and tissue types. Liver THg ranged from 0.05 to 63.7 µg/g. Fetal and pup livers had significantly lower THg and TSe, higher percentage MeHg+, and greater range of molar TSe:THg than subadult and adult livers. Molar Se:MeHg+ ratios, including Se in excess of nonmethylmercury, were dependent on MeHg+ in fetuses and pups. While THg varied significantly by muscle type (heart vs. skeletal) and anatomical location, concentrations were strongly correlated. Biomagnification and/or bioaccumulation of THg in liver of older animals confounded comparison with other tissues; however, in fetal and pup liver THg correlated with other tissues. In contrast, liver MeHg+ correlated with other tissues across all age classes. Fetal and pup tissues, which reflect in utero exposure and are subject to limited bioaccumulation, are ideal for assessing mercury exposure related to dam diet, including intertissue comparison, and represent key cohorts of concern. Evaluating MeHg+ and TSe in tissues from multiple age cohorts allows better intertissue comparison, providing insight into time courses, routes of exposure, and potential for adverse effects. Environ Toxicol Chem 2022;41:1477–1489. © 2022 SETAC Chemically and physiologically driven differences in total mercury, monomethylmercury (MeHg+), and total selenium concentrations between age cohorts and tissues (organotropism) of Steller sea lions may confound comparisons between animals and tissues. A One Health perspective benefits from concurrent measurements of analytes. This is key to separating effects of long‐term bioaccumulation of non‐MeHg+; to interpreting more immediate routes of exposure, potential biotransformation of ingested mercury, and potential for adverse effects; and to assessing food security for pinniped consumers in Alaska. THg = total mercury; TSe = total selenium.