While warming and eutrophication have increased the frequency and magnitude of harmful cyanobacterial blooms globally, the scenario for many eutrophic tropical freshwaters is a perennial year-round bloom. Yet, the drivers of persistent blooms are less understood when conditions such as light, temperature, and nutrients favor cyanobacteria growth year-round, and especially in regions facing recurrent periods of drought. In order to understand the drivers of cyanobacteria dominance, we assessed the abiotic conditions related to the abundance and dominance of the two dominant bloom-forming genera Raphidiopsis and Microcystis, in six shallow, man-made lakes located in the semiarid Northeastern region of Brazil during a prolonged regional drought. Lower water level corresponded to increased phosphorous and nitrogen concentration and, consequently, phytoplankton biomass. Cyanobacterial biomass was also proportional to phosphorus concentrations during year-round blooms. Yet, the two dominant cyanobacterial genera, Raphidiopsis and Microcystis, seldom co-occurred temporally and the switch between them was driven by water transparency. Our results illustrate the effects of drought induced water level reductions on the biomass and composition of cyanobacterial blooms in tropical shallow man-made lakes. Given the ideal year-round conditions (i.e., high light and temperature), droughts may be expected to intensify the risk and multitude of problems associated with eutrophication.