The ongoing rise of atmospheric carbon dioxide is expected to continue increasing temperatures in aquatic ecosystems, with potentially profound impacts on aquatic microbiomes and ecosystem function. The Laurentian Great Lakes – an unparalleled natural resource, holding 20% of Earth’s surface freshwater – are particularly vulnerable, due to rapid warming and altered hydrology. Yet, astonishingly little is known about the microbiome of the Lakes and its potential response to rising temperatures. To address parts of this knowledge gap, I have helped to compiled a time-series of in situ observations from 2012-2019 to assess the historical relationship between temperature and community structure. In this presentation, I will share my latest results and discuss the implications this has on our understanding of how temperature shapes the Great Lakes microbial community.