Samples were obtained during the Schmidt Ocean Institute cruise "Exploring Fronts With Multiple Robots" to the Pacific Ocean in 2018 (https://schmidtocean.org/cruise/exploring_fronts_with_multiple_aerial-surface-underwater-vehicles/). This expedition target the Subtropical Front, located approximately 1,000 nautical miles off the coast of Southern California. A SEABIRD SBE 9 PLUS CTD profiler with sensors for water temperature, salinity, oxygen, fluorescence and turbidity was used during this expedition. CTD profiles were taken within water depths between 300 m and 500 m. In total, 126 CTD casts at different stations were run. The achieved data have been converted using the software SBE Data Processing. Water samples for microplankton analysis were also collected in some of the CTD stations using a multi water sampler (rosette) from the research vessel "Falkor" and concentrated on board in a 0.2 um Sterivex filter. Results from 18S and 16S amplicon sequencing are public available in ENA-EMBL archive with the project accession number PRJEB32783.