You can search and download 164 volumes of logbooks of the Royal Navy's voyages of scientific discovery, from series reference ADM 55. These volumes are the logs (navigational records) and journals (narrative accounts) of naval officers of ships engaged in exploration and surveying, which were used by the Hydrographic Office to produce charts and other data. Most of the logs were kept by naval captains, masters, lieutenants and masters' mates, although there are a few logs which were kept by boatswains or assistant surgeons. Amongst this collection of Royal Naval logs, there are a several logs which were kept by merchant ships. The records were made between 1757 and 1861, with one exception; the logs of the 'Morning' (ADM 55/163 and ADM 55/164), which were made in 1904. The main areas covered in the logs are the Pacific, the Arctic, the Antarctic, Australia, the Americas and the west coast of Africa, although China, St Helena and other places are also included. Many famous officers kept logs held in this collection, including James Cook, William Bligh and Matthew Flinders
http://www.nationalarchives.gov.uk/documentsonline/shipsonexploration.asp