Concentrations of 15 trace elements (aluminum, arsenic, cadmium, chromium, cobalt, copper, iron, lead, manganese, mercury, nickel, selenium, tin, vanadium, and zinc) were determined in vibrissae (whiskers) and serum of two sympatric pinniped species, the Peruvian fur seal population (PFS; Arctocephalus australis Peruvian subpopulation) and South American sea lion (SASL; Otaria byronia) at Punta San Juan, Peru during 2011-19 sampling events. Element concentrations were 2-20 times higher in vibrissae than in serum. Vibrissae and serum concentrations of several elements, including aluminum, arsenic, and lead, suggest that environmental contaminants may affect the health of pinnipeds at Punta San Juan. Although toxicity thresholds are unknown in pinnipeds, high concentrations of some elements (especially aluminum, arsenic, and lead) may have adverse impacts on their health such as immunosuppression and impaired reproduction. Arsenic was the only element that increased in mean vibrissae concentration throughout the study period. Female SASL vibrissae contained a mean arsenic concentration three times higher than the male SASL vibrissae mean arsenic concentration, and twice as high as the arsenic mean for all PFS vibrissae. The mean male SASL vibrissae cadmium concentration was five times higher than the vibrissae cadmium mean for both PFS males and females and nearly three times higher than the vibrissae cadmium mean for SASL females. Serum concentrations of aluminum, arsenic, copper, and manganese were significantly higher during moderate to extreme El Niño years compared to La Niña years. With stronger and more frequent El Niño-Southern Oscillation events predicted in the future, it is vital to understand how these trace elements may affect pinniped population health.