We examined the diurnal to seasonal dynamics of the sea surface partial pressure of carbon dioxide (pCO2) in a subtropical nearshore estuarine system, Hangzhou Bay, adjacent to the Changjiang Estuary in the vicinity of the East China Sea, based on data collected between July 30, 2010 to September 20, 2011 by a surface buoy equipped with an autonomous pCO2 system along with hydrological and other chemical sensors. The study site (122.37° E, 30.55° N) is influenced by the river plumes of both the Changjiang and Qiantang River and is characterized by strong tidal circulation and highly turbid waters. The amplitude of pCO2 changes increased from winter to summer over both diurnal and spring-neap tidal cycle timescales. The average surface water pCO2 was slightly undersaturated with respect to the atmosphere in winter (382 ± 18 μatm), but supersaturated in spring (500 ± 56 μatm) and summer (687 ± 110 μatm). Overall the study site was a source of atmospheric CO2 with an average sea to air flux of 14 ± 9 mmol C m−2 d−1 from January to October 2011. We revealed factors controlling the pCO2 dynamics at different timescales. Over seasonal timescales, temperature and estuarine mixing dominated the seawater pCO2 variability. Over spring-neap tidal timescales in winter and spring, the major drivers were similarly water mass mixing and temperature. However, in summer, biological activity and air-sea exchange became the two principal factors controlling the variations in surface seawater pCO2. Our mass balance models further suggested that biological processes impacted surface pCO2 differently during different tidal phases. Respiration was revealed to promote the increase in pCO2 during spring tide in August, but in neap tides of the same month biological production was evident and resulted in the drawdown of pCO2. This is because photosynthesis was generally limited by light in summer at the study site due to high turbidity, except during neap tides when turbidity was dramatically drawn down, triggering high biological productivity. At the diurnal timescale, sea surface pCO2 was primarily controlled by tidal mixing, except during neap tides in summer when sea surface pCO2 was greatly influenced by biological metabolism. This study also revealed significant inter-summer differences between 2010 and 2011, showing lower sea surface pCO2 in August 2010 as compared to August 2011, which was likely due to the enhanced biological uptake as a result of the relatively low turbidity caused by weak tidal currents and enhanced river flow in August 2010. Our study highlights a highly dynamic system primarily driven by tidal mixing, which not only modulates water mass mixing but also affects turbidity, which subsequently controls biological production. These processes led to a synergy of CO2 dynamics in a tidally driven and highly turbid nearshore system, where high frequency time-series observations are essential to reveal the complex controls of CO2 dynamics.