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Abstract Most work on how estuarine dynamics impact dissolved oxygen (DO) distributions has focused on tides, but in shallow estuaries with large fetch or small tides, wind can be the primary mixing agent and also drives advection. To investigate how these processes affect DO distributions, an observational study was conducted in the shallow, microtidal Neuse Estuary. Salinity, DO, and velocity profiles were measured at multiple positions along and across the estuary over a 6‐month period. A one‐dimensional model (General Ocean Turbulence Model) provided additional insight into the response of salinity and DO to wind. Salinity and oxygen conservation equation terms were calculated from observations and simulations. Cross‐estuary wind drove lateral circulation and tilted the isohalines, reducing stratification; lateral advection and enhanced mixing reduced vertical gradients and increased the bottom DO. Down‐estuary wind tended to increase the exchange flow and stratification, but concurrently the surface wind‐mixed layer deepened over time. The balance of these processes determined if the water column became fully mixed or remained stratified, and the depth of the pycnocline and oxycline. An expression for steady state surface layer thickness was derived by considering the competition between the horizontal and vertical buoyancy flux, and the predictions agreed well with observations and simulations. Up‐estuary wind inhibited the exchange flow and the combination of advection and mixing homogenized the water column. While these patterns generally held for purely across‐ or along‐channel wind, the response was often more complex as the wind vector varied in orientation and with time.