Little is known about the molecular and physiological function of co-occurring microbes within freshwater cyanobacterial harmful algal blooms (cHABs). To address this, community metatranscriptomes collected from the western basin of Lake Erie during August 2012 were examined. Using sequence data, we tested the hypothesis that the activity of the microbial community members is independent of community structure. Predicted metabolic and physiological functional profiles from spatially distinct metatranscriptomes were determined to be >90% similar between sites. Targeted analysis of Microcystis aeruginosa, the historical causative agent of cyanobacterial harmful algal blooms over the past ϳ20 years, as well as analysis of Planktothrix agardhii and Anabaena cylindrica, revealed ongoing transcription of genes involved in microcystin toxin synthesis as well as the acquisition of both nitrogen and phosphorus, nutrients often implicated as independent bottom-up drivers of eutrophication in aquatic systems. Transcription of genes involved in carbon dioxide (CO 2 ) concentration and metabolism also provided support for the alternate hypothesis that high-pH conditions and dense algal biomass result in CO 2 -limiting conditions that further favor cyanobacterial dominance. Additionally, the presence of Microcystis-specific cyanophage sequences provided preliminary evidence of possible top-down virus-mediated control of cHAB populations. Overall, these data provide insight into the complex series of constraints associated with Microcystis blooms that dominate the western basin of Lake Erie during summer months, demonstrating that multiple environmental factors work to shape the microbial community. F reshwater ecosystems are considered among the most endangered in the biosphere (1). One threat to fresh waters around the world is the now nearly annual occurrence of blooms of toxic cyanobacteria. Molecular signatures of cyanobacterial harmful algal blooms (cHABs) have been identified on all seven continents, and these blooms have been occurring with increased frequency and duration in recent years (2-4). The accumulation of bloom biomass has been associated with fish, avian, and mammal intoxication (5, 6); the formation of hypoxic zones (7); the production of taste and odor compounds (8, 9); and even human liver failure in extreme cases (10).The Laurentian Great Lakes are an important freshwater resource, holding ϳ18% of the world's potable water and ϳ84% of the surface waters in North America (11). cHABs have had a persistent presence in Lake Erie and other Laurentian Great Lakes for several decades (3, 12, 13). Nuisance biomass and toxin production associated with cHABs in the Great Lakes have had a detrimental effect not only on ecosystem health but also on the economic health of the surrounding communities; indeed, in August 2014, a bloom event led to the shutdown of the water supply for some ϳ500,000 residents in the region of the city of Toledo, OH (14). To date, research efforts have broadly identified nutrient inputs an...