The dataset contains Nd isotope signatures (expressed as εNd) and Pb isotopic ratios (206Pb/204Pb, 207Pb/204Pb, 208Pb/204Pb) for IODP 383 Site U1541, DSDP 85 Site 574, ODP 138 Site 846, ODP 189 Site 1172 measured in fish debris, foraminifera and bulk leachates. The data analyzed using a MC-ICP-MS cover the Late Miocene from 9.0 to 5.2 Ma BP. The obtained deep South Pacific εNd (authigenic) values for the Late Miocene are consistently more radiogenic than presently implying a changed deep water mass exchange with higher influence of Pacific Deep Water, similar to observations of the Early and Middle Pliocene.