We studied dissolved organic matter (DOM) dynamics in the sea surface microlayer (SML) during a mesocosm study at the Sea sURface Facility (SURF) of the Institute for Chemistry and Biology of the Marine Environment (ICBM) in Wilhelmshaven, Germany (53.5148 °N, 8.1463 °E). The study was conducted from 18 May to 16 June 2023 as part of the multidisciplinary BASS research unit (Biogeochemical processes and Air-sea exchange in the Sea-Surface microlayer). SURF was filled with pretreated natural seawater from the nearby Jade Bay (53° 28' 42'' N, 8° 12' 15'' E) to replicate natural conditions. We selected this approach to examine the regrowth of surviving phytoplankton cells after the initial water treatments, simulating a native microbial community starting with almost no bioproduction or pre-existing bioproduction products. To induce and maintain the phytoplankton bloom, inorganic nitrogen, phosphorus, and silicate were added on May 26, May 31, and June 01, 2023. By that, we induced an algal bloom of Emiliania huxleyi and Cylindrotheca closterium. Water samples were collected using a glass plate for the SML and a tube at 40 cm depth for the underlying water (ULW). This dataset contains DOM molecular data from ultrahigh-resolution mass spectrometry (Fourier-transform ion cyclotron resonance mass spectrometer, FT-ICR-MS), molecular indices calculated from FT-ICR-MS data (Ibio, Iphoto, IDEG) and environmental data, including dissolved organic carbon (DOC) and dissolved organic nitrogen (DON). Furthermore, it contains attenuated total reflectance Fourier Transform Infrared (ATR-FTIR) data from representative samples for each bloom phase. By combining molecular analyses with nutrient and bloom-phase data, we highlight the in situ production of carbohydrate-like and laminarin-derived DOM as a significant contributor to SML composition. General metadata from the multidisciplinary mesocosm study, including temperature, salinity and chlorophyll a, are provided in Bibi et al. on PANGAEA at the following link: doi:10.1594/PANGAEA.984101.