This dataset consists of 20 CTD cast profiles from 20 stations in the Whittard Canyon and Haig Fras marine conservation zones, as part of the CodeMAP (Complex Deep-sea Environments: Mapping habitat heterogeneity As Proxy for biodiversity) project. These data were collected aboard the RRS James Cook cruise JC125 (Chief Scientist Veerle Huvenne), which departed and returned to Southampton from 09 August 2015 to 12 September 2015. The cruise was conducted to carry out habitat mapping work in the Whittard Canyon and Haig Fras to obtain a better insight in the biodiversity patterns, benthic habitat distributions and sediment transportation processes of submarine canyons. The CTD profile data collected supports data from marine geology, ecology, remote sensing and underwater vehicle technology to establish an integrated, statistically robust, and fully 3D methodology to map complex deep-sea habitats. Parameters measured from the CTD profiles include: pressure, depth, temperature, practical salinity, dissolved oxygen, chlorophyll-a fluorescence, transmittance, attenuance and turbidity. Data were collected using a ship deployed stainless steel CTD frame mounted with the following equipment: Sea-Bird 911plus CTD System, Digiquartz pressure sensor, Sea-Bird 3plus premium temperature sensor, Sea-Bird 4C conductivity sensor, Sea-Bird 43 dissolved oxygen sensor, WET Labs ECO BB(RT)D backscattering sensor, Chelsea Technologies Group Aquatracka III fluorometer, Chelsea Technologies Group Alphatracka II transmissometer (25 cm path length). The CTD data were received by the British Oceanographic Data Centre (BODC) having been binned into 2 m 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 European Research Council to CodeMAP (Grant No 258482).