This dataset comprises the following water body parameters: pressure; density; salinity; temperature; fluorescence; oxygen; dissolved inorganic nutrients; dissolved inorganic carbon (DIC); particulate carbon (PC); particulate organic carbon (POC); particulate nitrogen (PN); alkalinity; pH; chlorophyll; photosynthetically active radiation (PAR); delta 15 N isotopic composition of PN and nitrate; delta 13 C isotopic composition of POC; delta 18 O isotopic composition of nitrate; ratio of oxygen isotopes. This dataset also includes dissolved inorganic nutrients in sediment pore water, and major and minor element concentrations in sediment. Data were sampled on the West Antarctic Peninsula (WAP), more specifically in Ryder and Marguerite Bays. Measurements were obtained from either in situ sensors, samples collected by box coring, or by Niskin bottles mounted on the CTD rosette of RRS James Clark Ross during cruises JR20141231 (JR307, JR308) and JR15003 which took place from 31 December 2014 to 07 January 2015 and from 17 December 2015 to 13 January 2016 respectively. Samples were also collected from Niskin bottles deployed with a hand-cranked winch or 12 V electric bilge pump from a rigid-hulled inflatable boat between 16 November 2013 and 21 March 2016. Sediment samples were analysed for major and minor element composition by X-ray fluorescence spectroscopy at the School of Geosciences, University of Edinburgh. This research project aimed to examine the ways in which ongoing climate change and sea ice decline at the WAP impact upon nutrient budgets and biogeochemical cycling throughout the region, and to trace the movement and modification of circumpolar deep water across the WAP shelf and its influence on macronutrient and inorganic carbon supply to productive coastal regions. Data were generated by Sian Henley (University of Edinburgh), Hugh Venables and Michael Meredith (British Antarctic Survey), Elizabeth Jones (University of Groningen), Katharine Hendry (University of Bristol), and Yvonne Firing (NOC Southampton), with funding from NERC Independent Research Fellowship (NE/K010034/1), the University of Edinburgh School of Geosciences, the British Antarctic Survey Polar Oceans Program, the Netherlands Polar Program (NOW), British Antarctic Survey CGS-109, and NERC NC Funding for SR1b repeat transect (PI Firing). Additional contributors to the dataset were Malcolm Woodward (Plymouth Marine Laboratory), Melanie Leng (British Geological Survey) and Colin Chilcott and Nicholas Odling (University of Edinburgh).