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. Seawater samples were collected using 10 L Niskin bottles attached to the CTD Rosette. Duplicate samples for dissolved organic carbon (DOC) and total dissolved organic nitrogen (TDN) were filtered through 0.45 μm GMF GD/X filters (Whatman, GE Healthcare Life 248 Sciences, UK) and collected in combusted glass ampoules. Syringes and filters were rinsed with 25 and 50 mL of sample, respectively in order to remove potential contaminations. Samples were acidified with 20 μL of hydrochloric acid (30%) and stored at 4°C until analysis by high−temperature combustion using a Shimadzu TOC−VCSH after Engel & Galgani (2016). Values of TDN were corrected with dissolved inorganic nitrogen (nitrate+nitrite) and thereafter referred to as dissolved organic nitrogen (DON). To estimate the fraction of semi-labile dissolved organic carbon and semi-labile dissolved organic nitrogen, we determined high-molecular-weight (>1 kDa) dissolved combined carbohydrates (dCCHO) based on Engel and Händel (2011, https://doi.org/10.1093/plankt/fbq122) and dissolved hydrolysable amino acids (dHAA) based on Lindroth and Mopper (1979, https://doi.org/10.1021/ac50047a019) and Dittmar et al, (2009). The analysis of DCCHO detected 11 monomers: and the dHAA analysis classified 13 monomers. The calculations for the carbon and nitrogen contents of dCCHO and dHAA were based on carbon and nitrogen atoms contained in the identified monomers. The sum of dCCHO and dHAA carbon and nitrogen contents are referred to as SL-DOC and SL-DON respectively.