Based on the investigation of biomass and the measurement of CO2 and CH4 fluxes, the CO2 exchanges between mangrove- and shoal wetland ecosystems and atmosphere in Guangzhou were studied, and the CO2 absorption capability of the wetlands vegetation net productivity as well as the carbon sink function of the wetlands under different waterlogged conditions (perennial, intermittent, and no water-logging) was analyzed. As for mangrove wetland ecosystem, its vegetation net productivity absorbed 33.74 t x hm(-2) x a(-1) of CO2, and soil emitted 12.26 t x hm(-2) x a(-1) of CO2 (including the greenhouse effect amount of CH4 converted into that of CO2,) illustrating that mangrove wetland had a 21.48 t x hm(-2) x a(-1) net absorption of CO2, being a strong carbon sink. For shoal wetland ecosystem, its vegetation net productivity absorbed 8.54 t x hm(-2) x a(-1) of CO2, and soil emitted 5.88 t x hm(-2) x a(-1) of CO2 and 0.19 t x hm(-2) x a(-1) of CH4. If converting into carbon, the wetland absorbed 2.33 t C x hm(-2) x a(-1), and soil emitted 1.74 t C x hm(-2) x a(-1) (including the carbon in CH4), illustrating that shoal wetland fixed 0.59 t C x hm(-2) x a(-1), being a weak carbon sink. If the greenhouse effect amount of CH4 was converted into that of CO2, the soil emitted 9.78 t x hm(-2) x a(-1) of CO2, which was 1.24 t x hm(-2) x a(-1) more than the absorption. As a result, shoal wetland was a weak carbon source. Between the two test greenhouse gases, CH4 was the main one emitted under perennial water-logging, while CO2 was that under no water-logging. Moreover, the wetland under perennial water-logging had the strongest carbon sink function, while that under no water-logging was in adverse.