Methods used to estimate community primary production and respiration in intertidal environment are still subject of controversy. Underwater community respiration (CR), net production (NCP) were calculated from simultaneous in situ measures of change in oxygen (O-2), dissolved inorganic carbon (DIC) and carbon dioxide (CO2) concentration in benthic chambers performed in February, April, July and November on a Zostera noltii bed. The CRQ (CRDIC/CRO2) and CPQ (NCPo2/NCPDIC) varied between 0.15 and 3.07 and between 0.03 and 6.83, respectively. Carbon fluxes calculated from CO2 measurement were greatly underestimated, representing only 0.4-5.9% of fluxes estimated from DIC measurement. Indeed, CO2 or HCO3- input or uptake by seagrass community affect the proportions of all the chemical components of dissolved inorganic carbon (DIC, the sum of free dissolved CO2, carbonic acid H2CO3, bicarbonate and carbonate ions, HCO3- and CO32-). Thus, CO2 method is not reliable. O-2 measurement does not take into account anaerobic respiration through chemical oxidation and simultaneous O-2 and DIC measurements should be favored to calculate CRQ and CPQ which need to be discussed in marine environment at community scale.