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Although cyanobacterial harmful algal blooms (CHABs) are promoted by nutrient loading and elevated temperatures, the effects of these processes on bloom diversity are unclear. This study used traditional and next-generation sequencing approaches to assess shifts in phytoplankton, cyanobacterial (16S rRNA), and microcystin-producing (mcyE) communities during CHABs in western Lake Erie (Maumee and Sandusky Bays) in response to natural and experimental gradients of nitrogen (N), phosphorus (P), and temperature. CHABs were most intense near the Maumee and Sandusky Rivers and were dominated by Microcystis and Planktothrix, respectively. Sequencing of 16S amplicons revealed cryptic cyanobacterial diversity (47 genera) including high abundances of two distinct clades of Synechococcus in both bays and significant differences in community structure between nutrient-rich nearshore sites and less eutrophic offshore sites. Sequencing of mcyE genes revealed low taxonomic (n = 3) but high genetic diversity (n = 807), with toxigenic strains of Planktothrix being more abundant than Microcystis and more closely paralleling microcystin concentrations. Cyanobacterial abundance significantly increased in response to elevated N, with the greatest increases in combined high N, P, and temperature treatments that concurrently suppressed green and brown algae. N significantly increased microcystin concentrations and the relative abundance of nondiazotrophic genera such as Planktothrix, while diazotrophic genera such as Dolichospermum and Aphanizomenon were, in some cases, enhanced by high P and temperature. While nutrients and elevated temperatures promote CHABs, differing combinations selectively promote individual cyanobacterial genera and strains, indicating management of both N and P will be required to control all cyanobacteria in Lake Erie, particularly as lake temperatures rise.