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The present study aims to understand the mechanisms controlling ecosystem metabolic states and atmospheric CO2 fluxes and explore their linkages through monthly investigations along the tropical Kaoping Submarine Canyon (KPSC) in southwestern Taiwan. The magnitudes of integrated gross production (IGP) and integrated dark community respiration (IDCR) were higher in summer than in winter, likely supported by greater inputs of freshwater in summer with high loads of nutrients and organic carbon. Strong positive correlations were observed between gross production (GP) (or dark community respiration (DCR)) and temperature, photosynthetically active radiation and nutrients, but negative correlations were observed between GP (or DCR) and salinity in discrete water samples; these results reveal the significant impacts of freshwater inputs on GP and DCR. GP was determined largely by DCR, and DCR was attributed largely (78%) to bacterial respiration in the KPSC. Approximately 60% of measurements were autotrophic conditions (IGP/IDCR > 1) in most wet seasons except for certain offshore stations, which were apparently driven by higher temperature and nutrient availability, whereas 40% of measurements revealed heterotrophic conditions (IGP/IDCR < 1) in most offshore stations. The air-sea fluxes of CO2 revealed that about 64% of all measurements were sinks of atmospheric CO2, but those sinks did not completely coincide temporally with autotrophic conditions. Biological controls [GP correlated significantly with nutrients and chlorophyll a and was primarily determined by DCR] and temperature effects may overwhelmingly dictate metabolic states and air-sea fluxes of atmospheric CO2, respectively, though the combined effects were evident in this coastal ecosystem. The study may shed light on implications of recent increases in nutrient inputs for shifting the coastal ecosystem from heterotrophic to autotrophic conditions, and the global warming per se may increase the chance for tropical coastal ecosystems acting as a source of atmospheric CO2.