We measured fluxes of carbon dioxide (CO(2)), methane (CH(4)), and nitrous oxide (N(2)O) simultaneously in two typical fringing zones, sandy shore and salt marsh, of coastal lagoon, Lake Nakaumi, Japan, in mid-summer 2003. Our aim was to quantify net the greenhouse gases (GHGs) fluxes and examine key factors, which control variation of the GHGs fluxes in the two sites. Net CO(2) and CH(4) fluxes were markedly different between the two sites; magnitudes and variations of the both fluxes in sandy shore were lower than those of salt marsh. Meanwhile, magnitude and variation of net N(2)O flux in the two sites were similar. In sandy shore, temporal and spatial variation of the three GHGs fluxes were highly controlled by water level fluctuation derived from astronomic tide. In salt marsh, spatial variation of the three GHGs fluxes were correlated with aboveground biomass, and temporal variation of CO(2) and CH(4) fluxes were correlated with soil temperature. The sum of global warming potential, which was roughly estimated using the observed GHGs fluxes, was ca. 174-fold higher in salt marsh than in sandy shore.