This dataset consists of 6 CTD profiles from 6 stations in the Whittard Canyon, collected as part of the HERMONIE (Hotspot Ecosystem Research and Man's Impact on European seas) and OCEANS 2025 projects. These data were collected aboard the RRS James Cook cruise JC036 (Chief Scientist Douglas Masson), which departed Brest, France, on 19 June 2009 and arrived in Southampton, UK, on 28 July 2009. The biological and geological research programme was built around a series of ROV video transects to determine variations in species and community structure and composition in different geological and topographic settings down the canyon. Additional coring, CTD and water column particulate sampling programmes were planned to investigate the recent geological history of the canyon and investigate sediment accumulation in the canyon. Macro and meiofauna were also sampled in areas of soft substrate. The sensors used for the CTD profiles include temperature, conductivity, pressure, oxygen, fluorescence, altitude, irradiance, backscatter, and attenuance. Data were collected using a ship-deployed Sea-Bird 911plus CTD System mounted with the following equipment: Sea-Bird SBE 3plus (SBE 3P) temperature sensors, Sea-Bird SBE 4C conductivity sensors, Paroscientific Digiquartz depth sensor, Sea-Bird SBE 43 Dissolved Oxygen Sensor, Chelsea Technologies Group Aquatracka III fluorometer, Chelsea Technologies Group 2-pi PAR irradiance sensors, WET Labs {Sea-Bird WETLabs} ECO BB(RT)D backscattering sensor and Chelsea Technologies Group Alphatracka II transmissometer. The CTD data were received by the British Oceanographic Data Centre (BODC) having been binned into 2m depth profiles for the downcast. The data have been processed and quality controlled using in-house BODC procedures and are available to download from the BODC website. Funding was provided by the Natural Environment Research Council (NERC).