Carbon and nutrient cycles in large temperate lakes such as Lake Erie are primarily driven by phototrophic and heterotrophic microorganisms, although our understanding of these is often constrained to late spring through summer due to logistical constraints. During periods of >90% ice-cover in February of 2008, 2009 and 2010, we collected samples from an icebreaker for an examination of bacterial production as well as microbial community structure. In comparison with summer months (August 2002 and 2010), we tested hypotheses concerning seasonal changes in microbial community diversity and production. Bacterial production estimates were ~ 2 orders of magnitude higher (volume normalised) in summer relative to winter. Our observations further demonstrate that the microbial community, including single celled phototrophs, varied in composition between August and February. Sediment traps deployed and collected over a three year period (2008 - 2011) confirmed that carbon export was ongoing and not limiting winter production. The results support the notion that active primary producers in winter months export carbon to the sediments that is not consumed until the warmer seasons. The establishment of this linkage is a critical observation in efforts to understand the extent and severity of annual summertime formation of a zone of regional hypoxia in Lake Erie. This article is protected by copyright. All rights reserved.