Acidification in subsurface coastal waters has received global attention. It is now generally accepted that intensive organic matter degradation fueled by eutrophication leads to excessive dissolved inorganic carbon (DIC) and reduced pH, while the quantification of influencing factors is not fully addressed. In this study, a coupled physical-biogeochemical model is established to investigate the seasonal variations and controlling factors of pH and aragonite saturation (Ω_arag) in the semi-closed Bohai Sea (BS). The results indicate that the seasonal variations of alkalinity in bottom water remain steady, while DIC increases sharply in summer, corresponding to a decrease in pH and Ω_arag. Acidification occurs in the depressions around the central bank with differences between the northern and southern low pH cores. Biological processes and vertical diffusion dominate acidification, with dramatic stratification as a precondition for its development. Accumulation of DIC explained 80% of the variation in the acidified zones, while alkalinity mitigates the variations near the estuary. In addition, sensitivity experiments also show that different concentrations of riverine TA and DIC bring different evolutionary processes in summer, especially near the estuary. The study advances formation mechanisms of coastal acidification and provides a basis for the subsequent prediction and management.