In the Mediterranean Sea, an accumulation of dissolved organic matter (DOM) is observed during the stratified summer period, which is decoupled from the spring phytoplankton maxima. We hypothesize that DOM composition in summer changes its composition, from labile DOM in spring to recalcitrant prokaryote-derived compounds during the summer accumulation period. To test this, we tracked the seasonality of DOM molecular composition and chemical diversity using Fourier transmission-ion cyclotron resonance Mass Spectrometry (FT-ICR MS) from 2019 to 2021 in a monthly sampled time series in the NW Mediterranean Sea. This dataset presents this DOM data, presented as the lists of all molecular formulae per sample with, their absolute and relative intensity per analytical triplicate and their mass to charge ratios.