Carbon dioxide and methane emissions from estuaries are reviewed in relation with biogeochemical processes and carbon cycling. In estuaries, carbon dioxide and methane emissions show a large spatial and temporal variability, which results from a complex interaction of river carbon inputs, sedimentation and resuspension processes, microbial processes in waters and sediments, tidal exchanges with marshes and flats and gas exchange with the atmosphere. The net mineralization of land-and marsh-derived organic carbon leads to high CO 2 atmospheric emissions (10-1000 mmol•m -1 ), except in vegetated tidal flats and marshes, particularly those at freshwater sites, where sediments may be CH 4 -saturated. CH 4 emissions from subtidal estuarine waters are the result of lateral inputs from river and marshes followed by physical ventilation, rather than intense in-situ production in the sediments, where oxic and suboxic conditions dominate. Microbial oxidation significantly reduces the CH 4 emissions at low salinity (<10) only.