These data were collected as part of the scientific agenda of the United Nations Development Program (UNDP) and sponsored by the Secretary of Environment and Sustainable Development of Argentina (http://www.ambiente.gov.ar). The project Coastal Pollution Prevention and Marine Biodiversity Management (Project 28385-AR-UNDP-ARG/02/018l) also referred to as GEF Patagonia was partially funded by the Global Environment Facility (GEF), with additional funding from the Inter-American Institute for Global Change Research (CRN061 and 2076). The project goal was to determine the seasonal variability of physical-chemical properties of highly productive regions of the southwest South Atlantic continental shelf. The GEF Patagonia field experiments consisted of three oceanographic cruises carried out on board R/V ARA PUERTO DESEADO, in October 2005 (PD GEFPAT_1), and March (PD GEFPAT_2) and September 2006 (PD GEFPAT_3). In each cruise, hydrographic stations were occupied along cross-shelf sections spanning the shelf and extending to the onshore edge of the western boundary currents between 38° and 55°S. This submission reports the CTD and thermosalinograph data collected during the three GEF Patagonia cruises.