The Caspian seal (Pusa caspica) is an endangered species that only lives in the Caspian Sea. Little information is available on its exposure to contaminants, and no data exists for Southern sub-populations. From 2011 to 2016, tissues samples were collected from 20 Caspian seals to (i) Define the concentration of trace elements in five different matrices and the concentration of 30 pesticides in their blubber; (ii) Determine whether differences in contaminant concentrations are age- or sex-related; (iii) Evaluate if detected concentrations can represent a risk to the species. Age- and sex-related variations were detected for Zn and Hg in the blubber and Fe in the kidney by age only. Exceptionally high Hg concentrations and low levels of hepatic Zn were detected, raising some concern about the reproductive health of seals. Similarly, the DDTs levels detected were in the range of adverse reproductive effects in marine mammals. Based on these results, potentially adverse effects on the immune and endocrine systems of the Caspian seal cannot be ruled out. Therefore, it is of the utmost importance that pollutant monitoring becomes an integral component of conservation strategies for the Caspian seal.