This dataset consists of 147 CTD profiles that were collected during the Mission Arctic citizen science sailing expedition to western Greenland, Nares Strait, and Baffin Bay. These data were collected in July-September 2017. A RBR Concerto CTD (https://rbr-global.com/) that measured conductivity, temperature, and pressure was used in fjords from Paamiut to Upernavik in July 2017. A Sontek CastAway CTD (https://www.sontek.com/castaway-ctd) was used for all stations north of Upernavik in western Greenland and on the return leg along the western shore of Baffin Bay to St. John's, Newfoundland. All CTD profiles have been quality controlled to remove spikes, surface soak, and the upcast. The remaining downcast data were averaged in 0.5 m bins and stored in a single network common data form (netCDF) file that also contains the time, latitude, and longitude for each cast.