Datasets used for the analyses reported in the manuscript titled "Biogeochemical dynamics in adjacent mesoscale eddies of opposite polarity". For all files, the suffix HL4 indicates the expedition HOE-LEGACY 4, while the suffix MESOSCOPE indicates the MESO-SCOPE expedition. Temperature profiles measured underway across adjacent eddies are saved in files UnderwayTemperature*.csv. Station coordinates are saved in UnderwayCoordinates*.csv Shipboard vertical profiles of dissolved oxygen, chlorophyll fluorescence, and potential density anomaly are saved in files TransectOxygen*.csv, TransectFluorescence*.csv, and TransectSigma*.csv, respectively. Station coordinates are saved in TransectCoordinates*.csv Inorganic nutrient concentrations measured across adjacent eddies are saved in files EddyNutrients*.csv. Particulate carbon, chlorophyll a, beam attenuation, and chlorophyll fluorescence in the eddy centers are saved in file ParticlePigmentComparison_15m.csv and ParticlePigmentComparison_DCM.csv for the depth of 15 m and the depth of the DCM, respectively. Cell counts from flow cytometry in the eddy centers are saved in files FlowCytometry_cyclone_*.csv and FlowCytometry_anticyclone_*.csv. This files also report the depth of the DCM for each eddy center. Imaging FlowCytobot (IFCb) measurements during MESO-SCOPE are reported in files IFCB_Class_DCM&15m_MESOSCOPE.csv for classes and IFCB_Genera_DCM_MESOSCOPE.xlsx for genera.