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. Particulate organic carbon and nitrogen were analyzed according to Sharp (1974; https://doi.org/10.1371/journal.pone.0131538). Transparent exopolymer particles (TEP) and Coomassie blue stainable particle (CSP) were measured by the microscopic method after Engel et al. (2009; Determination of Marine Gel Particles , Practical guidelines for the analysis of seawater. / ed. by Oliver Wurl Boca Raton [u.a.] ; CRC Press, ISBN: 978-1-420-07306-5 ). spectral slope of the particle size distribution were calculated after Mari, X. and Kiørboe, T. (1996). Abundance, size distribution and bacterial coloniza− tion of transparent exopolymeric particles (TEP) during spring in the kattegat. J. Plankton Res., 18(6):969–986.