a b s t r a c t The role of coastal lagoons and estuaries as sources or sinks of inorganic carbon in upwelling areas has not been fully understood. During the months of MayeJuly, 2005, we studied the dissolved inorganic carbon system in a coastal lagoon of northwestern Mexico during the strongest period of upwelling events. Along the bay, different scenarios were observed for the distributions of pH, dissolved inorganic carbon (DIC) and apparent oxygen utilization (AOU) as a result of different combinations of upwelling intensity and tidal amplitude. DIC concentrations in the outer part of the bay were controlled by mixing processes. At the inner part of the bay DIC was as low as 1800 mmol kg À1 , most likely due to high water residence times and seagrass CO 2 uptake. It is estimated that 85% of San Quintín Bay, at the oceanic end, acted as a source of CO 2 to the atmosphere due to the inflow of CO 2 -rich upwelled waters from the neighboring ocean with high positive fluxes higher than 30 mmol C m À2 d À1 . In contrast, there was a net uptake of CO 2 and HCO 3 À by the seagrass bed Zostera marina in the inner part of the bay, so the pCO 2 in this zone was below the equilibrium value and slightly negative CO 2 fluxes of À6 mmol C m À2 d À1 . Our positive NEP and DDIC values indicate that Bahía San Quintín was a net autotrophic system during the upwelling season during 2005.