Freshwater ecosystems are sentinels for changes in terrestrial and atmospheric processes and provide critical ecosystem and economic services. The Laurentian Great Lakes (LGL) represent environmentally diverse, hydrologically connected ecosystems where primary production can be similar to that in the Sargasso Sea to more mesotrophic production with reoccurring harmful algal blooms. The LGLs have been exposed to numerous environmental perturbations that have altered water quality, primary producers, nutrient composition, and water clarity and may fundamentally alter primary productivity and downstream processes and communities across the LGL. Our lab investigates the Chicagoland area of Lake Michigan to better understand how microbes respond to ongoing and future disturbances in these ecologically and economically critical habitats.