The dataset contains CTD data collected during the MN249 Cruise (10-20 September 2023), in the frame of the Horizon 2020 Project ‘Developing Optimal and Open Research Support for the Black Sea’ (DOORS) financed by the European Commission (EC), through the Horizon 2020 Call: H2020-BG-2018-2020 (Blue Growth). The main objectives of the cruise were to look at the impact of the methane released from the anoxic sediment on the water column from a geochemistry and microbial biodiversity point of view and to map the upper part of the hydrate stability zone of the gas hydrates by identifying the methane-sulfate transition zone within the sediments and also to measure the heat flow within the sediments (mainly in presence of gas hydrate). For water column investigation, 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).