The present study represents the first time-series evaluation of air-sea CO 2 exchange for a coastal marine system of a subtropical high island of the Pacific. From September 2003 through September 2004, surface water total alkalinity (TA) and dissolved inorganic carbon (DIC) data were collected bimonthly throughout the Kaneohe Bay estuarine-coral reef system. The partial pressure of carbon dioxide (pCO 2 ) and the air-sea CO 2 exchange flux were calculated using TA, DIC, atmospheric CO 2 at sea level, and five wind speed relationships for gas transfer velocity. pCO 2 values were above the atmospheric level (average: 378 μatm) throughout Kaneohe Bay (400-500 μatm) and Kaneohe Stream waters (600-1300 μatm) during baseline conditions. pCO 2 levels above atmospheric in bay water were driven mainly by calcification while pCO 2 levels above atmospheric in stream water were driven mainly by remineralization of terrestrial organic matter. pCO 2 values above the atmospheric level were observed in surface water that extended almost 4 km beyond the boundary of the bay indicating that processes inside the bay such as calcification affect the inorganic carbon properties of the surrounding near shore open ocean. Precipitation from storm events in the Kaneohe watershed increases stream and land runoff that brings excess nutrients to bay waters. These excess nutrients stimulate phytoplankton blooms which draw down CO 2 in Kaneohe Bay water through photosynthesis. Despite the significant effects of the storms, Kaneohe Bay was a net annual source of CO 2 to the atmosphere of -0.046 Gmol C year -1 (-0.55 kton C year -1 ) with an area-specific flux of -1.45 mol C m -2 year -1 (-17.4 g C m -2 year -1 ). The source of CO 2 in Kaneohe Bay could be stronger on a long-term basis since dry years may be stronger net annual sources than wet years such as this study period. As shown by Kaneohe Bay data, the dynamic nature of estuarine systems makes closely spaced time-series data imperative for characterizing accurately the inorganic carbon system and the net annual air-sea exchange flux of CO 2 .