Examining the physical processes that control dissolved oxygen (DO) on timescales ranging from days to weeks is necessary to comprehend the intra-seasonal hypoxic variability in coastal waters. Wind-driven circulation and stratification can rapidly alter low-DO conditions both spatially and temporally in regions of freshwater influence (ROFIs), but our understanding is limited by a lack of high frequency observations. Here, we combine continuous moored time series (30 min resolution) with spatial surveys conducted during summer 2019 to investigate the physical controls on hypoxia variability in the Mississippi Bight, northern Gulf of America, a seasonally stratified, river-influenced shelf. Summer 2019 was characterized by severe hypoxic conditions which experienced intraseasonal fluctuations throughout the season driven by wind forcing. The inner shelf experienced expanding hypoxia due to upwelling-favorable winds advecting low-DO waters both onshore and eastward along the shelf over 3-7 days periods. The offshore passage of Hurricane Barry temporarily disrupted hypoxia through wind-driven mixing, but stratification and hypoxia re-established within days after storm, with a density front setting up the control of the cross-shelf pattern of DO recovery. Inertial oscillations from diurnal sea-breeze/land-breeze cycles may potentially contribute to low-DO variations by raising pycnocline shear and the possibility of intermittent mixing at higher frequencies through their interaction with the background geostrophic flow. These results demonstrate that Ekman circulation, storm disturbances, and near-inertial dynamics can be drivers of intra-seasonal hypoxic variability in ROFIs, providing insight for improved management and forecast methods in river-dominated coastal systems.