We present water column thermal structure for two climatically different years: 2012, which experienced abnormally warm spring and summer air temperatures preceded by a relatively low ice winter and 2013, which experienced cooler than average spring and average summer air temperatures and preceded by average ice conditions. Mean bottom water temperatures for the season and during cold water intrusions were significantly warmer in 2012 than 2013 leading to a significantly reduced stratified season in 2012. Cold water intrusions were driven into southern Green Bay by southerly winds while intrusions were terminated when winds switched to persistent northerly winds. 2012 observed a significant increase in northerly winds relative to 2013, decreasing cold water intrusion presence and duration but winds did not fully explain the difference in thermal conditions for southern Green Bay. These cold bottom waters drive stratification in polymictic southern Green Bay while dimictic waters were found to have significantly warmer bottom temperatures during 2012 and a deeper mixed layer. Our observations suggest that relatively shallow (<20 m), seasonally stratified systems may not increase in stratification strength and duration under a warming climate; rather, changing wind climatology and surface heat flux can inform the degree to which the mixing regime can be expected to change and impact stratification and thermal structure of coastal systems. We discuss the biogeochemical implications of different thermal regimes, particularly within the context of multiple drivers of physical water column structure in eutrophic, stratified coastal systems.