The initiation, bloom, and bust of harmful Cyanobacteria and algae blooms (HAB) in lakes are controlled by top-down and bottom-up ecological controls. Excess phosphorous and nitrogen inputs from anthropogenic sources are primary to blame, but eukaryotic grazers may also promote or curb Cyanobacteria dominance. We tracked shifts in bacterial composition, lake chemistry, and eukaryotic grazing community weekly or bi-weekly through spring and summer and modeled the causes of specific Cyanobacterial species blooms and busts across three lakes in Utah, USA, with differing lake trophic states. Regardless of trophic status, all three lakes experienced blooms of varying composition and duration. Aphanizomenon strain MDT14a was the most dominant species in every bloom on Utah Lake, comprising up to 44.16% of the bacterial community. Utah Lake experienced a total of 18 blooms across all sites ranging in duration from one to six weeks. Phormidiaceae sp. (8.5  6.1%) and Microcystis sp. (9.7  4.7%) were the most abundant species in the Deer Creek bloom. Deer creek experienced one bloom at the beginning of fall. Nodularia sp. (9.7  2.1) dominated Great Salt Lake bloom. The Great Salt Lake experienced four separate blooms during the summer months that lasted one to three weeks. Phosphorous concentrations on Utah Lake varied across site and season. Nitrate concentrations on Deer Creek increased over season with a ten-fold increase in concentration. We characterized Cyanobacteria blooms as either bloom communities (growing populations of Cyanobacteria) or as bust communities (declining populations of Cyanobacteria). Using these designations, we modeled the growth and decline of the Cyanobacteria populations across season with top-down and bottom up-controls. Based on generalized least-squared modeling, eukaryotic grazing does not affect relative Cyanobacteria abundances as much as nutrient limitations. Aphanizomenom strain MDT14a was positively correlated with temperature (P < 0.028) and the concentration of K (P = 0.007) and negatively correlated with increases in conductivity (P = 0.0088). Microcystis was positively correlated with increasing levels of SRP (P < 0.001) and negatively correlated with higher Ca concentrations (P = 0.008) and PP (P = 0.008). Busts of Microcystis were related to decreases in nitrate (P = 0.06) and lower total lake depths (P = 0.03). Phormidiaceae sp. relative abundance was negatively correlated with higher levels of TDN (P = 0.01-0.001) and Mg (P = 0.01) and positively correlated with higher S concentrations (P = 0.007). Our findings suggest that micronutrients and more bioavailable forms of P may potentially allow Cyanobacteria to break dormancy and proliferate HAB communities.