This is processed and corrected Conductivity, Temperature, Depth (CTD) data from the Transkei Shelf Oceanography Cruise on the Algoa 241, 12 July to 11 August, 2017. The area covered includes the Transkei shelf and continental slope (20m to 1000m), of the Eastern Cape, between Cape St Francis and Port Shepstone in the South-West Indian Ocean.Our knowledge of the distribution of offshore benthic biodiversity on the Transkei shelf is very limited. The region between Algoa Bay and Port Edward is not only important for understanding the functioning of existing Marine Protected Areas (MPAs) such as Pondoland, Dwesa-Cwebe, and the Amathole, but is of particular relevance to the new Operation Phakisa proposed MPA network that will potentially include additional MPAs such as the Protea Banks, Amathole Expansion, and the proposed Addo MPA. In addition, further knowledge is needed to support decision-making about the offshore extent of the Dwesa-Cwebe MPA. The oceanography in the form of water column and energy characteristics, circulation regimes and biological production all play critical roles in determining biodiversity patterns, as does connectivity along this shelf. Using a similar approach, this project follows the successful African Coelacanth Ecosystem Programme (ACEP) II Kwa-Zulu Natal (KZN) Bight project between 2010 and 2013 that investigated the ecosystem processes on the KZN Bight linking geological, biological and physical processes to understand ecosystem functioning. This dataset was processed using older standards which may not align with international best practices and the standards currently adhered to by the Department of Forestry, Fisheries and the Environment (DFFE). The Department is re-processing and replacing data to ensure everything has the same format and is of the same quality and datasets will be marked as obsoleted once that is done. As such the user assumes the entire risk related to the use of these data in its current state and format. DFFE disclaims all warranties of the data whether expressed or implied, including without limitation, any warranties of merchantability or fitness for a particular purpose. For any concerns regarding the data, the user may decide to liaise with the listed PIs who will share their insight on the data quality, where possible. It is also strongly recommended that the user liaises with the listed PIs regarding their proposed projects to mitigate against duplication of research efforts.