The dataset contains CTD data collected during the MN248 Cruise (1-10 September 2023), at the sampling stations located in the Romanian Black Sea area, in the framework of H2020 DOORS Project. The main goal of the cruise was to assess the sediment nutrients cycling capacity and the influence of faunal activity on benthic turnover rates of nutrient and oxygen through ex-situ sediment core incubation. The data acquisitions were focused on three main benthic habitats, as follows: coarse and mixed biogenic type of substrata suitable for thriving of mussel’s biogenic reefs and mud sediments under river plume influence. For water column characterization, at each sampling station, a SBE 911Plus Sealogger CTD with specific sensors and a SBE 32 Rosette water sampler with 12 of 5 liters Niskin bottles were deployed to measure physical & chemical water parameters (temperature, salinity, oxygen, fluorescence, pH, turbidity and other derived parameteres).