Successions of lake ecosystems from clear-water, macrophyte-rich conditions into turbid states with abundant phytoplankton have taken place in many shallow lakes in China. However, little is know about the change of carbon fluxes in lakes during such processes. We conducted a case study in Lake Biandantang to investigate the change of carbon fluxes during such a regime shift. Dissolved aquatic carbon and gaseous carbon (methane (CH4) and carbon dioxide (CO2)) across air–water interface in three sites with different vegetation covers and compositions were studied and compared. CH4 emissions from three sites were 0.62±0.36, 0.70±0.36, and 1.31±0.57mgm−2 h−1, respectively. Correlation analysis showed that macrophytes, rather than phytoplankton, directly positively affected CH4 emission. CO2 fluxes of three sites in Lake Biandantang were significantly different, and the average values were 77.8±20.4, 52.2±14.1 and 3.6±26.8mgm−2 h−1, respectively. There were an evident trend that the larger macrophyte biomass, the lower CO2 emissions. Correlation analysis showed that in different sites, dominant plant controlled CO2 flux across air–water interface. In a year cycle, the percents of gaseous carbon release from lake accounting for net primary production were significantly different (from 39.3% to 2.8%), indicating that with the decline of macrophytes and regime shift, the lake will be a larger carbon source to the atmosphere.