Climate change is expected to affect marine mercury (Hg) biogeochemistry and biomagnification. Recent modeling work suggested that ocean warming increases methylmercury (MeHg) levels in fish. Here, we studied the influence of El Niño Southern Oscillations (ENSO) on Hg concentrations and stable isotopes in time series of seabird blood from the Peruvian upwelling and oxygen minimum zone. Between 2009 and 2016, La Niña (2011) and El Niño conditions (2015–2016) were accompanied by sea surface temperature anomalies up to 3 °C, oxycline depth change (20–100 m), and strong primary production gradients. Seabird Hg levels were stable and did not co-vary significantly with oceanographic parameters, nor with anchovy biomass, the primary dietary source to seabirds (90%). In contrast, seabird Δ199Hg, proxy for marine photochemical MeHg breakdown, and δ15N showed strong interannual variability (up to 0.8 and 3‰, respectively) and sharply decreased during El Niño. We suggest that lower Δ199Hg during El Niño represents reduced MeHg photodegradation due to the deepening of the oxycline. This process was balanced by equally reduced Hg methylation due to reduced productivity, carbon export, and remineralization. The non-dependence of seabird MeHg levels on strong ENSO variability suggests that marine predator MeHg levels may not be as sensitive to climate change as is currently thought.