The dataset contains Nd isotope signatures (expressed as εNd) and Pb isotopic ratios (206Pb/204Pb, 207Pb/204Pb, 208Pb/204Pb) for IODP Expedition 383 Sites U1540 and U1541 measured in fish debris, foraminifera and bulk leachates. The data covers the Early and Middle Pliocene from 3.2 to 5.2 Ma BP. Additionally, lithogenic εNd, Pb isotopic ratios (206Pb/204Pb, 207Pb/204Pb, 208Pb/204Pb), and Sr isotopic ratio (87Sr/86Sr) for the sortable silt fraction (<63 µm) for U1540 and U1541 are included. The obtained South Pacific εNd (authigenic) values for the Pliocene cover a range from εNd= -7.5 to -5.5 and with it are consistently more radiogenic than presently implying a changed deep water mass exchange. The authigenic Pb isotopic signatures lie in a range between 206Pb/204Pb=18.76 to 18.79 207Pb/204Pb=15.64 to 15.66 and 208Pb/204Pb= 38.70 to 38.78 and indicate changes in weathering input to the South Pacific.