We quantified Δ14C, δ
18O, and δ
13C cycles along ontogeny within four bay scallop (Argopecten purpuratus) shells collected from Callao Bay, Salaverry, and Sechura Bay, Peru following the 1907–1908 non-El Niño years and the 1925–1926 El Niño. Δ14C and δ
13C generally covary; Δ14C and δ
18O vary inversely. Simultaneous decreases in Δ14C and increases in δ
18O in non-El Niño shells are followed by constant Δ14C and gradually decreasing δ
18O, which we interpret as evidence for discrete marine upwelling events followed by warming of the initially cold upwelled water. Upwelling changes from El Niño events are detectable with difficulty in mollusk shell Δ14C.