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Abstract A unique combination of data collected from fixed instruments, spatial surveys, and a long‐term observing network in the Hudson River demonstrate the importance of spatial and temporal variations in atmospheric gas flux. The atmospheric exchanges of oxygen (O₂) and carbon dioxide (CO₂) exhibit variability at a range of time scales including pronounced modulation driven by spring‐neap variations in stratification and mixing. During weak neap tides, bottom waters become enriched in pCO₂and depleted in dissolved oxygen because strong stratification limits vertical mixing and isolates sub‐pycnocline water from atmospheric exchange. Estuarine circulation also is enhanced during neap tides so that bottom waters, and their associated dissolved gases, are transported up‐estuary. Strong mixing during spring tides effectively ventilates bottom waters resulting in enhanced CO₂evasion and O₂invasion. The spring‐neap modulation in the estuarine portion of the Hudson River is enhanced because fortnightly variations in mixing have a strong influence on phytoplankton dynamics, allowing strong blooms to occur during weak neap tides. During blooms, periods of CO₂invasion and O₂evasion occur over much of the lower stratified estuary. The along‐estuary distribution of stratification, which decreases up‐estuary, favors enhanced gas exchange near the limit of salt, where vertical stratification is absent. This region, which we call the estuarine gas exchange maximum (EGM), results from the convergence in bottom transport and is analogous to the estuarine turbidity maximum (ETM). Much like the ETM, the EGM is likely to be a common feature in many partially mixed and stratified estuarine systems.