Western Long Island Sound (wLIS) has experienced a long-term decline in the July/August summer minima bottom dissolved oxygen concentrations. This decline continues despite New York City having eliminated routine raw discharges of sewage, upgraded sewage treatment to nearly complete secondary, and introduced nitrogen control. It is our conclusion that long-term changes in physical oceanographic processes are having an impact on the hypoxia problem in wLIS. Specifically, we show that interannual variations in summertime thermal and haline stratification contribute to variations in vertical mixing which controls the ventilation of bottom waters. Analyses of bottom dissolved oxygen and density stratification point directly to the importance of wind-induced current shear in controlling stratification and vertical mixing; numerical simulations support this result. Interannual variations in both the direction and directional constancy of summertime winds over wLIS are shown to control the ventilation of bottom waters and thereby the seasonal development of hypoxia.