These CTD profiles were taken by RV Senckenberg of the Senckenberg Research Institute in the framework of the MGF-North Sea project at the German Exclusive Economic Zone (EEZ) of the North Sea. There, the NATURA2000 sites Amrumbank (AMB), Sylt Outer Reef (SAR), Borkum Reef Ground (BRG) and Dogger Bank (DOG) were visited in 2020, 2021 and 2022. At each station, a CTD probe (Sea & Sun Technologies, CRD48) was lowered to the seabed, recording temperature and salinity each second. The dataset was trimmed and thus contains the records from each station during the individual heaving phases. Altogether, the dataset contains data from eight cruises. Namely they are (with month / year in brackets) [and number of stations in square brackets]: BRG20 (July 2020) [14], SAR20 (May 2020) [19], AMB21 (August 2021) [11], DOG21 (July 2021) [11], SAR22 (May 2022) [15], BRG22 (July 2022) [14], AMB22_1 (July 2022) ([11] and AMB22_2 (October 2022) [10].