This paper presents time-series data collected from four shallow mooring stations located in the inner part of Mobile Bay, Alabama, during the passage of Hurricane Ivan in September 2004. Sharp changes in salinity and its gradient were observed in the open part of Mobile Bay even before Ivan landed. Increases in water level (2.20–2.43 m) and salinity (7–11 practical salinity units) during the passing of Ivan were large enough to double mean depths and background salinities, respectively, in the relatively secluded areas of the Mobile-Tensaw Delta. Large diel variations in dissolved oxygen, as large a daytime increase as 9.7 g m⁻³, were observed in the Mobile-Tensaw Delta after landfall of Ivan. Community metabolism rates estimated using the diel oxygen curve method show that both the production and the respiration rates increased by 2–3 times after Ivan passed, suggesting that supersaturation dissolved oxygen conditions in the afternoon were the result of high primary production driven by storm-enhanced input of nutrients and that low dissolved oxygen conditions in the following morning were the result of high community respiration of storm-enhanced input of organic matter from benthic sediments and inundated wetlands.