Relationships between shifts in climatic and other environmental conditions and changes in the character and dynamics of phytoplankton blooms were examined in three interconnected subtropical lagoons on the east coast of Florida, i.e., Mosquito Lagoon, Indian River Lagoon, and Banana River Lagoon, from 1997 to 2013. Phytoplankton blooms were a common feature through most of the study period in two of the lagoons. From 1997 to 2009, blooms in the latter two lagoons were typically dominated by dinoflagellates in the warm wet season and diatoms in the cool dry season. Blooms of the dominant bloom-forming dinoflagellate species Pyrodinium bahamense were positively correlated to rainfall levels, indicating a link to enhanced external nutrient loads. In 2011–2013, major blooms were observed in all three lagoons, but unlike the previous 14 years, they were dominated by picoplanktonic eukaryotes, including a chlorophyte, Pedinophyceae sp., and the brown tide species Aureoumbra lagunensis. The results suggest that extreme climatic conditions, including record cold winter water temperatures and low rainfall levels, were major driving factors in this state shift in the character of blooms, through a wide range of effects including die-offs of benthic flora and fauna, suppression of grazer populations, alteration of nutrient regimes, and uncharacteristic water column conditions, such as elevated salinities and light attenuation.