Pelagic ecosystems are changing due to environmental and anthropogenic forces, with uncertain consequences for the ocean's top predators. Epipelagic and mesopelagic prey resources differ in quality and quantity, but their relative contribution to predator diets has been difficult to track. We measured mercury (Hg) stable isotopes in young (<2 years old) Pacific bluefin tuna (PBFT) and their prey species to explore the influence of foraging depth on growth and methylmercury (MeHg) exposure. PBFT total Hg (THg) in muscle ranged from 0.61 to 1.93 μg g-1 dw (1.31 μg g-1 dw ±0.37 SD; 99% ± 6% MeHg) and prey ranged from 0.01 to 1.76 μg g-1 dw (0.13 μg g-1 dw ±0.19 SD; 85% ± 18% MeHg). A systematic decrease in prey δ202Hg and Δ199Hg with increasing depth of occurrence and discrete isotopic signatures of epipelagic prey (δ202Hg: 0.74 to 1.49‰; Δ199Hg: 1.76-2.96‰) and mesopelagic prey (δ202Hg: 0.09 to 0.90‰; Δ199Hg: 0.62-1.95‰) allowed the use of Hg isotopes to track PBFT foraging depth. An isotopic mixing model was used to estimate the dietary proportion of mesopelagic prey in PBFT, which ranged from 17% to 55%. Increased mesopelagic foraging was significantly correlated with slower growth and higher MeHg concentrations in PBFT. The slower observed growth rates suggest that prey availability and quality could reduce the production of PBFT biomass.