This dataset comprises of physical oceanographic parameter measurements and meteorological data collected as part of the British Antarctic Survey (BAS) South Orkney Ecosystem Studies project from RRS James Clark Ross cruise JR15004. Data were collected surrounding the South Orkney Islands within the Scotia Sea, and coverage was between 19/01/2016 until 21/02/2016. This dataset contains downcast Conductivity Temperature Depth (CTD) profiles from 45 stations, and measurements of underway navigation, meteorology and sea surface hydrography through the ship's underway system. Measurements include water temperature, conductivity, photosynthetically active radiation (PAR), transmittance, fluorescence and oxygen concentrations, as well as air temperature, humidity, atmospheric pressure, total incidence radiation (TIR), wind speed and direction. The data collected during the cruise were used to examine the factors that determine the distribution of krill and other pelagic organisms across a range of time and space scales. All data were collected by originators at the British Antarctic Survey, the National Oceanic and Atmospheric Administration (NOAA) Southwest Fisheries Science Center, and the Institute of Marine Research, Norway.