This dataset contains the results of the fluorescent dissolved organic matter characterisation (FDOM) and water mass optimum multiparameter analysis from the MAFIA cruise (Migrants and Active Flux In the Atlantic ocean). Samples were collected in the tropical and subtropical Atlantic during the MAFIA cruise (April 2015) on board the BIO Hespérides. Seawater samples for biogeochemical analyses were collected at 13 stations (from the Brazilian coast to the Canary Islands), from the surface down to 3500 m, using a General Oceanics oceanographic rosette equipped with 24 l PVC Niskin bottles. Fluorescence measurements were performed with a Perkin-Elmer LS55 spectrofluorometer and FDOM was characterised by means of a Parallel Factor analysis. The contribution of each water mass to each sample was objectively quantified applying an optimum multiparameter analysis (excluding mixed layer samples, here < 100 m). The aim of this dataset was to jointly characterise the FDOM and water mass distributions to infer the processes that shape the dissolved organic matter pool in the deep ocean (water mass mixing and history vs local processes).