The constraint of air-sea CO₂ fluxes and their variability in coastal oceans at different timescales and spatial scales is at the base of the controversy concerning their role in the global carbon cycle. The lack of high-resolution sampling of the partial pressure of CO₂ (pCO₂) would largely underestimate monthly air-sea CO₂ fluxes, even reverse the direction of the fluxes at annual level. However, mechanistic understanding towards the diurnal to weekly dynamics of pCO₂ remains challenging due to the complicated interaction of biogeochemical and physical forcings in coastal waters. Here we examined the short-term variability of sea surface pCO₂ recorded by a Battelle Seaology pCO₂ Monitor amounted on a buoy located in the outer Pearl River estuary, a large subtropical estuary system in the northern South China Sea, from July 2 to August 11, 2015. Surface seawater pCO₂ was highly variable, ranging from 78 to 640 μatm with an average of 279 μatm, mostly ~100 μatm lower than the atmospheric pCO₂. On diel timescales, pCO2 changes of ~40-100 μatm occurred in response to diurnal primary production and respiration; temperature and tidal effects played a minor role. Over longer timescales, pCO₂ was influenced by atmospheric forcing, physical advection and biological metabolism. For example, a surface cooling of ~3 ˚C and increase in pCO₂ of ~110 μatm occurred after Typhoon Linfa passed near Hong Kong on July 9, 2015. The increase in pCO₂ probably resulted from enhanced upward mixing of high-salinity, rich-inorganic carbon subsurface water. Subsequently, intense plume due to typhoon-induced strong freshwater discharge, coupled with elevated biological productivity, reduced pCO₂ back to the pre-typhoon level. Overall, freshwater inputs, wind-driven upwelling and biological processes were the main drivers of short-term variability of pCO₂ in the subtropical estuary, in contrast to temperate coastal ecosystems mostly subject to the thermal and tidal effects. Net fluxes of CO₂ for the observation period (-4.8 mmol CO₂ m^-2 d^-1) were directed from atmosphere to ocean, but with a wide range from ~-30 to +20 mmol CO₂ m^-2 d^-1 depending largely on wind speed. We also found that gas exchange direction between the air-sea interface was closely related to wind direction when strong wind events occurred. Therefore, careful consideration of the short-term variability of surface seawater pCO₂ and wind regime was needed to accurately estimate air-sea CO₂ fluxes in the subtropical estuary system.