Analysis of summer surface wind fields over the Laurentian Great Lakes from 1980 to 1999 show a statistically significant shift in wind direction beginning around 1990. Directional changes in the average wind field over the Great Lakes basin are consistent with a southward migration of the dominant summer storm track. In Green Bay (NW Lake Michigan), we show that the new wind field has most likely resulted in a decrease in water mass exchange with Lake Michigan leading to a decrease in bottom water hypoxia, warmer bottom water temperatures and an increase in benthic microbial metabolism.