Cyclone‐induced mixing and stratification shape autumnal hypoxia in a temperate estuary

Autumnal hypoxia in temperate estuaries is often overlooked due to its smaller extent, weaker intensity, and sparse observations compared to summer. However, climate variability may alter its seasonality. Using 40 yr (1984–2023) of hypoxic volume data from the Chesapeake Bay, combined with numerical simulations, we examined interannual drivers of autumnal hypoxia. September wind speeds were negatively correlated with hypoxic volume ( r = −0.49, p < 0.01), reflecting wind‐driven destratification. Conversely, September river discharge showed a strong positive correlation with October hypoxia ( r = 0.81, p < 0.01), indicating that lagged freshwater inputs from late‐season cyclones enhance stratification and re‐establish hypoxia. Model simulations of a representative tropical cyclone confirmed this dual effect that storm winds temporarily alleviated hypoxia, but subsequent river inflows prolonged it into October. Model results highlight that physical processes largely regulate autumnal hypoxia dynamics, and suggest that more frequent intense cyclones under climate change may increase its persistence.