Common loons (Gavia immer) staging on the Great Lakes during fall migration are at risk to episodic outbreaks of type E botulism. Information on distribution, foraging patterns, and exposure routes of loons are needed for understanding the physical and ecological factors that contribute to avian botulism outbreaks. Aerial surveys were conducted to document the spatiotemporal distribution of common loons on Lake Michigan during falls 2011–2013. In addition, satellite telemetry and archival geolocator tags were used to determine the distribution and foraging patterns of individual common loons while using Lake Michigan during fall migration. Common loon distribution observed during aerial surveys and movements of individual radiomarked and/or geotagged loons suggest a seasonal pattern of use, with early fall use of Green Bay and northern Lake Michigan followed by a shift in distribution to southern Lake Michigan before moving on to wintering areas. Common loons tended to occupy offshore areas of Lake Michigan and, on average, spent the majority of daylight hours foraging. Dive depths were as deep as 60 m and dive characteristics suggested that loons were primarily foraging on benthic prey. A recent study concluded that round gobies (Neogobius melanostomus) are an important prey item of common loons and may be involved in transmission of botulinum neurotoxin type E. Loon distribution coincides with the distribution of dreissenid mussel biomass, an important food resource for round gobies. Our observations support speculation that energy transfer to higher trophic levels via gobies may occur in deep-water habitats, along with transfer of botulinum neurotoxin.