Various forms of shallow gas have been observed in seafloor strata, on the seabed and in the water column during acoustic profiling investigations in 2007–2009 in Xiamen Bay and adjacent areas. Acoustically transparent zones, acoustic turbidity and gas seepage can be seen in seabed strata, pockmarks and accumulation bodies have been found on the seafloor, and hummocky features and mushroom shaped gas signatures can be identified in the water column. This evidence shows that shallow gas is widely distributed in and around Xiamen Bay, due to degradation of the organic matter transported by the Jiulong River. The area covered by such features is roughly estimated at 150 km2, and methane flux is estimated to be 150 × 106 m3 assuming the thickness of gas bearing formations to be 1 m. This study shows that even small rivers flowing out onto a continent shelf contribute to recognizable methane flux and are linked to identifiable gas reservoirs in the shallow seabed. More detailed studies are required to understand the role of such systems as a component of the global carbon cycle.