Abstract: Harmful cyanobacterial blooms (cyanoHABs) have occurred in lakes without development in different regions of the globe; dynamics and drivers of these blooms remain understudied. CyanoHABs alter the composition of bacterial communities with increases in specific cyanobacteria strains as well as shifts in heterotrophic taxa. These community shifts during cyanoHABs can be somewhat predictable but have been only studied in limited number of lakes, all highly productive and impacted by development. The Cascade Mountains (USA) offer a novel setting to examine cyanotoxin variation, as well as associated shifts in bacterial communities, across elevational and latitudinal gradients in relatively undeveloped lakes with documented cyanoHABs. Using physicochemical measurements, time-integrated toxin monitoring, and 16S rRNA sequencing of bacterial, we explored possible associations of bacterioplankton communities with cyanoHABs and toxins within a season and across lakes. We sampled three lakes biweekly in the ice-free season of 2020. Microcystin concentrations exceeded concentrations of 1ppb in two lakes at different points in the summer, during which cyanobacteria exceeded 20% of the bacteria community. The richness and evenness of the bacterial community decreased significantly with the onset of a cyanoHAB event, while lakes without cyanoHAB events did not exhibit any significant shifts in alpha diversity. During cyanoHAB events, bacterial community composition diverged significantly from communities outside of a cyanoHAB event, including those from the same lake, and varied based on microcystin concentrations. These compositional differences were not only driven by shifts in cyanobacteria, specifically from the order Nostocales, but also heterotrophic bacteria such as from the orders Burkholderiales, Cytophagia and Rhodospirillales. Therefore, bacterial community composition can be indicative of cyanoHABs and cyanotoxin prevalence across lakes spanning a trophic gradient.