Observations from the York River Estuary, Virginia, demonstrate that the along-channel wind plays a dominant role in governing the estuarine exchange flow and the corresponding increase or decrease in vertical density stratification. Contrary to previous findings that suggest wind stress acts predominantly as a source of energy to mix away estuarine stratification, our results demonstrate that the wind can play a more important role in straining the along-channel estuarine density gradient. Down-estuary winds enhance the tidally-averaged vertical shear, which interacts with the along-channel density gradient to increase vertical stratification. Up-estuary winds tend to reduce, or even reverse the vertical shear, reducing vertical stratification. In two experiments each lasting approximately a month, the estuarine exchange flow was highly correlated with the along-channel component of the wind. The changes in stratification caused by the exchange flow appear to control the amount of vertical mixing as parameterized by the vertical eddy viscosity. The degree of stratification induced by wind straining also appears to play an important role in controlling the effectiveness of wind and tidal mixing.