This dataset includes measured and calculated data over the epi-mesopelagic layer (0-450 m depth) of 29 stations with 4 stations within a cyclonic eddy nearby Brava island, 5 stations within a cyclonic eddy nearby Sal island, and one station within an anticyclonic eddy around the Cabo Verde islands in the eastern Tropical North Atlantic during the M160 cruise on the RV Meteor from November 22nd to December 20th, 2019. Virus like particles size classes and heterotrophic bacteria (low and high nucleic abundance) were measured by flow cytometry.