This dataset was compiled as part of a multiyear effort lead by Fisheries and Oceans Canada (DFO) to support sustainable aquaculture regulation in the Coast of Bays, an area of the south coast of Newfoundland. It is the second of a series aiming to provide an oceanographic knowledge baseline of the Coast of Bays. This dataset includes temperature, salinity, and dissolved oxygen concentration profiles collected during CTD surveys, each survey containing a varying number of casts/profiles taken within the area of interest. In total, 760 profiles from 11 surveys, executed over 276 stations, were collected from June 2009 to November 2013. Data were processed and quality controlled using the instrumentation manufacturer guidelines, custom tools as well as visual inspection. Data are provided in tab-delimited text-based format compatible with most data processing language and tools (e.g. MS. Excel) as well as with the Ocean Data View software (https://odv.awi.de/) for rapid visualisation. A summary of the CTD profiles and stations surveyed is also provided as a comma separated values (CSV) file. A full description of the data and of its use in the context of the motivating project can be found in http://www.dfo-mpo.gc.ca/csas-sccs/Publications/ResDocs-DocRech/2017/2017_077-eng.html. Analyses from this dataset were presented during a Canadian Science Advisory Secretariat (CSAS) meeting which took place in St John’s in March 2015 (http://www.dfo-mpo.gc.ca/csas-sccs/schedule-horraire/2015/03_25-26b-eng.html) and from which a Science Advisory Report (http://www.dfo-mpo.gc.ca/csas-sccs/Publications/SAR-AS/2016/2016_039-eng.html) and Proceedings (http://www.dfo-mpo.gc.ca/csas-sccs/Publications/Pro-Cr/2017/2017_043-eng.html) were published.