Lakes and reservoirs play key roles in global carbon cycling, especially as a carbon sink. Enrichment of nutrients in lakes and reservoirs (eutrophication) and rising global temperatures favors the proliferation of bloom-forming cyanobacteria. Harmful blooms of cyanobacteria (cyanoHABs) alter carbon and nutrient cycling in freshwater ecosystems. Some evidence suggests the introduction or establishment of invasive mussel species (i.e., Dreissena spp.) also favor cyanoHAB formation through selective filter feeding, a process through which they may also impact biogeochemical processes including carbon cycling and sequestration. However, few studies have considered the combined effects of invasive mussels and cyanoHABs on carbon and nitrogen cycling in freshwater ecosystems. Here, we examined microbial community composition and biogeochemical attributes (including carbon and nitrogen stable isotopes) in eutrophic lakes, reservoirs, and rivers in western Ohio, eastern Indiana, and northern Kentucky during the cyanobacterial bloom period of the summer of 2015. Our samples include both sites impacted by invasive mussels and those where invasive mussels have not yet been observed. Based on 16S and 18S rRNA gene sequence analysis, we found that cyanobacterial and algal communities varied across sites and were most closely related to habitat (sediment or water column sample) and site, regardless of the presence of invasive mussels or other environmental factors. However, we did find evidence that invasive mussels may influence both carbon and nitrogen cycling. While the results are based on a single time point sampling, they highlight the interactions of multiple environmental stressors in aquatic ecosystems and the critical need for more temporally intensive studies of carbon and nutrient cycling in bloom-and mussel-impacted waters.