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. Chromophoric and fluorescent dissolved organic matter were measured with a Shimadzu® 1800 UV−VIS double beam spectrophotometer and a Cary Eclipse Fluorescence Spectrophotometer respectively. The data included the absorption coefficient at 325 nm (a325) and the four fluorescent components obtained from PARAFAC analysis.