The Humboldt Current System along the Pacific coast of South America creates one of the most productive ecosystems on Earth. To trace the origin of the water masses in this area, we measured neodymium isotope compositions (ԑNd) in tooth enameloid of two genera of coastal sharks from latest Oligocene to early Pleistocene strata in the Pisco and Sacaco basins in southern Peru. Most ԑNd values range from −4 to −1, with a strong negative excursion in the late Miocene (∼8–7 million years ago [Ma]) with values as low as −9.2. The overall trend of the ԑNd values resembles that of equatorial Pacific deep waters, though with an offset of about +2 ԑNd units until about 6 Ma. With a major input of hinterland weathering considered unlikely, we interpret this pattern as reflecting a modern-type upwelling regime, though with a lower contribution of Antarctic waters than today. Starting about 6 Ma, the contribution of Antarctic waters to the upwelling waters increased approximately to present-day levels, coincident with, and possibly driven by, increased Antarctic glaciation and the Andes reaching their present-day elevation, both of which likely enhanced the counter-clockwise circulation in the South Pacific Ocean. The negative excursion of ԑNd values in the Pisco/Sacaco basins ∼8–7 Ma coincides with a late Miocene biogenic bloom in the Pacific Ocean and elsewhere, and with a strongly increased northward bottom current observed on the Nazca Drift System just offshore our sampling area. Thus, the negative excursion of ԑNd values in the Pisco/Sacaco basins likely resulted from a southern sourced input of nutrient-rich, unradiogenic water, which could have been an important contributor to the biogenic bloom.