The programme involved two major fieldwork activities: a deep ocean research cruise and a programme of freshwater studies. The marine component of the dataset generated a total of 430 distinct variables, quantifying the meteorology, hydrography, chemistry, biogeochemistry, and the microbial plankton (bacteria, phytoplankton and microzooplankton) biomass, taxonomic composition along the 5500 km cruise track in the Indian Ocean during August-September 2001. Measurements were mainly made on water samples collected either from the sea surface while the ship was underway or from a range of depths during conductivity-temperatue-depth (CTD) and water sampling stations at each of 11 sites occupied in the Indian Ocean. The maximum depth sampled at open ocean sites ranged from 300 to 3000 m. Short sections of 300 m deep CTD and fluorescence profiles were also obtained using a moving vessel profiler (MVP). The freshwater component of the dataset generated variables from Priest Pot in the Lake District and from a range of other freshwater sites around the UK. It contains underpinning weekly time-series measurements characterising the physical, chemical and biological condition of the water column at the Priest Pot sampling site between 2002-2004, together with data from studies focused on the seasonal and spatial dynamics of viruses, bacteria and picophytoplankton, trace metal distribution and the ubiquity of microbial protists. The database also contains 376 gene sequences from genetic material extracted from environmental samples. The programme was a 5-year Thematic Programme funded by the Natural Environment Research Council (NERC) and the purpose of the study was to improve understanding of aquatic microbial biodiversity, with the emphasis on community interactions, ecosystem function (e.g. biogeochemical cycling of carbon and nutrients, and the potential for biotechnological exploitation. The programme involved scientists from the Plymouth Marine Laboratory, the National Oceanography Centre Southampton, University of Cardiff School of Biosciences, University of Cardiff School of Earth and Ocean Sciences, University of Warwick School of Biological Sciences, University of Newcastle School of Civil Engineering and Geosciences, University of Bristol School of Biological Sciences, University of Oxford Department of Zoology, University of Liverpool School of Biological Sciences, University of Stirling School of Biological and Environmental Sciences, the Marine Biological Association of the UK, Lancaster University Department of Environmental Science and the Centre for Ecology and Hydrology (CEH) Lancaster and Dorset.