This dataset contains planktic foraminifera Trilobatus sacculifer and Dentoglobigerina venezuelana stable oxygen isotopes, Mg/Ca, local seawater δ18O and ΔT estimates from Site NGHP-01-01A, which was recovered by the drill ship JOIDES Resolution (JR) in the Kerala-Konkan Basin in the Eastern Arabian Sea (EAS; 15º18.366' N, 70º54.192' E; 2663 m water depth) during the Indian National Gas Hydrate Program (NGHP) Expedition 01 in 2006 (28.04.-19.08.2006). The data archived here was generated to reconstruct changes of the upper water column structure, i.e., depth of the mixed later and thermocline at Site NGHP-01-01A in the EAS during the middle Miocene in order to study changes in the summer South Asian Monsoon (SAM). The isotopic composition of the planktic foraminifera samples was analysed at the MARUM, University of Bremen, Germany, using a Finnigan MAT 251 mass spectrometer equipped with an automatic line for carbonate preparation (type "Kiel III"). Planktic foraminiferal trace element concentrations were measured using an Inductively Coupled Plasma Optical Emission Spectrophotometer (ICP-OES; Agilent 5110 VDV) at the Center of Major Equipment and Technology (COMET) of the State Key Laboratory of Marine Environmental Science (MEL), Xiamen University. Planktic foraminiferal Mg/Ca ratios were converted to temperature using the the multiple species planktic foraminifera calibration of Anand et al. (2003; doi:10.1029/2002PA000846). To account for past seawater Mg/Ca changes, the D. venezuelana and T. sacculifer Mg/Ca estimates were adjusted for changes in seawater Mg/Ca by modifying the Mg/Ca-temperature calibrations of Anand et al. (2003; doi:10.1029/2002PA000846), following Lear et al. (2015; https://doi.org/10.1002/2015PA002833. Seawater δ18O (δ18Osw) was calculated using the unadjusted and adjusted temperature Mg/Ca-temperature estimates in order to account for past seawater Mg/Ca changes by removing the temperature-driven component of the planktic foraminifera δ18O record. The δ18O-temperature relationship of (Bemis et al., 1998; https://doi.org/10.1029/98PA00070) was used to calculate the δ18Osw estimates. A local record of changes in δ18Osw was derived by subtracting an estimate of middle Miocene ice-volume changes from the δ18Osw record. In order to reconstruct the upper surface water column structure in the EAS, the difference in Mg/Ca-based temperatures (ΔT˚C) of surface-dwelling (Trilobatus sacculifer) and sub-thermocline-dwelling (Dentoglobigerina venezuelana) planktic foraminifera was calculated to estimate the upper ocean thermal gradient. The age model of all provided datasets is based on Yang et al. (2020; doi:10.1029/2020PA003853).