We examined the environmental and biological factors related to blooms of the toxic dinoflagellate Pyrodinium bahamense in three shallow, restricted subtropical lagoons in the Gulf of California during the rainy summer. In the San José, Yavaros, and El Colorado lagoons, the vegetative stage peaked at 63, 108, and 151 (×10 3 cells l -1 ), respectively. At San José, production of cysts peaked at 9.7×10 3 g -1 of dry sediment mass as the bloom declined. Large diatoms predominated, with P. bahamense the most common dinoflagellate during the blooms. Abundance of P . bahamense at San José was positively correlated with salinity (r=0.50, p=0.0003), seawater temperature (r=0.44, p=0.005), silicates (r=0.45, p=0.003), and ammonium (r=0.32, p=0.005), and negatively correlated with dissolved oxygen (r=-0.34, p<0.0001). No such correlations were found at El Colorado and Yavaros. The environmental window that favors development of blooms is restricted to the summer and is influenced by seawater temperature, salinity, and relative concentrations of ammonium and phosphates that, in turn, depend on rainfall and runoff, which is greater on the eastern side of the Gulf where seawater quality is degraded.