The North Yellow Sea (NYS) is a productive marginal sea of the western North Pacific. In summer and autumn, CaCO₃ saturation states beneath the seasonal thermocline in the NYS have frequently fallen below critical levels, indicating that marine calcifying organisms are under threat. To explore the long-term evolution of the acidification of the NYS, we reconstructed seasonal variations in subsurface aragonite saturation state (Ω_arag) and pH during 1976–2017, using wintertime and summertime temperature, salinity, dissolved oxygen and pH data mainly from a quality-controlled oceanographic database. Over the past 40 years, the wintertime warming rate in the NYS was twice the rate of global ocean surface warming. Warming-induced decrease in CO₂ solubility canceled out a part of the wintertime Ω_arag decrease caused by atmospheric CO₂ increase, and also had minor effect on pH changes in winter. Although the NYS is a semi-enclosed marginal sea, its interannual variations of wintertime temperature, salinity, pH and Ω_arag were correlated to Pacific Decadal Oscillation with a lag of 2–3 years. Due to the eutrophication-induced enhancement of net community respiration beneath the seasonal thermocline, long-term declines of bottom-water Ω_arag and pH in summer were substantially faster than the declines of assumed air-equilibrated Ω_arag and pH in spring. Over the past 40 years, the amplitudes of seasonal variations of bottom-water Ω_arag and pH from spring to summer/autumn have increased by 4–7 times. This amplification has pushed the NYS towards the critical threshold of net community CaCO₃ dissolution at a pace faster than that forecast under scenarios of atmospheric CO₂ increase. In summary, our results provide insights into the combined effects of ocean warming, eutrophication, atmospheric CO₂ rise and climate variability on coastal hydrochemistry, explaining how the environmental stresses on local marine calcifying organisms and the benthic ecosystem increased over the past 40 years.