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Coastal oceans are most likely to be impacted by anthropogenic activities because they are typically shallow and have more restricted water circulation than the open ocean. Kaneohe Bay served as a test site to gain insight into aspects of the carbon cycle. It is a semi-enclosed bay located on the eastern side of the island of Oahu, Hawaii and is the largest sheltered body of water in the islands. Thirteen profile stations were established and nine cruises were conducted during 2004-2009 on the R/V Kaholo. Cruises took place at various times of the year so that changes in carbon system parameters could be observed under varying conditions. Each cruise transect was 16 km long. This data set includes temperature, salinity, oxygen, pH, and other ancillary parameters.