This dataset consists of measurements of underway meteorology, navigation and sea surface hydrography. A comprehensive survey of the Southwest Indian Ocean, more specifically, the Southwest Indian Ridge (SWIR), was undertaken between 07 November 2011 and 21 December 2011 on the RRS James Cook cruise JC066. Navigation data were collected using an Applanix POSMV system and meteorology and sea surface hydrography were collected using the NMF Surfmet system. Both systems were run for the duration of the cruise, excepting times for cleaning, entering and leaving port, and while alongside. Data were collected as part of the NERC-funded project “Benthic Diversity of seamounts in the Southwest Indian Ocean”. The project aimed to describe and analyse the diversity and distribution of benthic assemblages, from meiofauna to megafauna, on seamounts in the central section of the SWIR between 41S, 42E and 33S, 58E. The NERC funded project was funded primarily by grant NE/F00504/1, with child grants NE/F006292/1 and NE/F005563/1. The lead grant is held at the University of Oxford, Department of Zoology, by Professor Alex David Rogers. The child grants are held at the natural History Museum, Life Sciences, by Dr Gordon Patterson, and the Scottish Asssociation for Marine Science, Dunstaffnage Marine Laboratory, by Dr Bhavani Narayanaswamy, respectively. Underway navigation, meteorology and sea surface hydrography data have been received as raw files by BODC and are available upon request.