The diurnal to weekly dynamics of carbon and oxygen in two productive tropical-subtropical nearshore shallow water systems were investigated using a combination of time-series observation and modeling. The two sites, Aodi (121.93uE, 25.06uN) and Nanwan (120.85uE, 21.91uN), were characterized by limited freshwater input, strong tidal advection and, at Nanwan, upwelling. The diurnal ranges were 96-234 mmol kg 21 for dissolved inorganic carbon (DIC), 8.9-42.2 Pa for partial pressure of carbon dioxide (pCO 2 ), and 37-239 mmol kg 21 for dissolved oxygen. The diurnal variability increased from spring to neap tidal states at both sites. A model accounting for gas exchange, biological activities, tidal advection, and upwelling was developed to assess the biophysical interactions modulating the biogeochemical dynamics. The strongest driver of the diurnal variability was the net ecosystem production of the benthic-dominated nearshore ecosystem. Tidal advection buffered the accumulation of biological effects and the intensified dispersion lowered the diurnal amplitudes at spring tides. Tide-induced upwelling at Nanwan increased the surface inorganic carbon, and its decreasing intensity resulted in declines in DIC and pCO 2 from spring toward neap tide. The maximum community photosynthetic rates at Aodi and Nanwan were 295 and 120 mmol C m 22 h 21 , with ecosystem respiratory rates of 122 and 53 mmol C m 22 h 21 . The two autotrophic ecosystems were sinks for atmospheric CO 2 during the study period, with the average air-sea fluxes being 20.30 and 20.56 mmol C m 22 d 21 for Aodi and Nanwan.