This dataset consists of physical oceanographic and meteorological data collected in the South Orkney Islands, Southern Ocean, onboard the RRS James Clark Ross during the period of 25 February 2016 until 25 March 2016 on JR15005 a South Orkney State of the Antarctic Ecosystem (SO-AntEco) cruise. Measurements were taken using conductivity-temperature-depth (CTD) profilers with attached auxiliary sensors, expendable bathythermographs (XBTs) and the ships underway monitoring system. Hydrographic profiles provide measurements of the water column, temperature, salinity, depth, conductivity, transmittance, fluorescence, irradiance, altimetry and dissolved oxygen. Underway measurements include meteorological, surface hydrography and navigational data. The data have been collected as part of the SO-AntEco project, a British Antarctic Survey (BAS) funded programme from 20 August 2015 to 24 August 2016 lead by Dr Huw Griffiths (BAS). This involved international collaboration with scientists from BAS, Scientific Committee for Antarctic Research (SCAR), Universities (Bristol, Hull, Liverpool and Oxford) and the Natural History Museum (NHM), London. This project was part of the wider SCAR biological research programme - State of the Antarctic Ecosystem (AntEco). The British Oceanographic Data Centre (BODC) hold CTD, XBT, navigation, meteorological and surface hydrographic data. The Polar Data Centre (PDC) at BAS are responsible for the long-term management of other datasets collected on cruise JR15005.