Seventeen sites in Florida Bay were sampled on a monthly basis for 51 months to describe the spatial and temporal patterns of phytoplankton blooms. The study focused on the picoplanktonic cyanobacterium Synechococcus. The greatest frequency and intensity of blooms was observed in the north‐central region of Florida Bay, where cellular biovolumes of this species regularly exceeded 10 × 106μm3 ml−1 and chlorophyll a concentrations were frequently >20 mg m−3. Synechococcus blooms were often restricted to this region of the bay, in part because of the network of shallow mudbanks and islands that restrict water exchange with other regions and outlying waters of the Atlantic Ocean and Gulf of Mexico. The most severe blooms occurred in the summer and fall (May–December). High concentrations of Synechococcus also appeared during the fall in the south‐central region of the bay. The appearance of blooms in this region coincided with the onset of seasonal cold fronts, whose strong northerly and northwesterly winds appear to drive bloom‐laden water from the north‐central region into adjacent parts of the bay. A number of physical and chemical factors appear to contribute to the remarkably high phytoplankton biovolumes observed in the north‐central region of Florida Bay. Physical factors include the shallowness and hydrological isolation of the region. The dominance of Synechococcus in the center of the bay may be attributable to several of the unique physicochemical characteristics of this species, including its small size, cyanobacterial metabolism, euryhaline character, buoyancy, and tolerance to high light intensity.

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Over the last half of the 20th century Pyrodinium bahamense var. bahamense has been observed in a variety of locations in the western North Atlantic. Recent evidence of the toxinproducing capacity of this variety of P. bahamense has heightened interest in its habitat requirements and preferences. The objective of this study was to examine the environmental factors that relate to the spatial and temporal patterns of the distribution and abundance of P. bahamense var. bahamense. Based on the results of this study we view the factors as operating in one or more ways: (1) ecophysiological limitations for survival and successful reproductive cycle, (2) environmental regulation of growth and standing crop, and (3) competitive advantages in relation to other species. The focus of the study was the Florida peninsula, but information from other environments in the tropical Atlantic and Gulf of Mexico was included in the interpretation of the results. In terms of physiological limitations, 20°C appears to be the lower temperature limit for a significant presence of P. bahamense var. bahamense, and the salinity tolerance ranged from 10 to 45. The bloom potential of P. bahamense var. bahamense was most closely associated with shallow ecosystems with long water residence times, and peak biomass levels were correlated to nutrient concentrations in regions of high abundance. The ability of P. bahamense var. bahamense to compete effectively for habitat with other euryhaline warm-water phytoplankton is viewed in terms of existing theories on succession and competition, including Margalef's Mandala, Reynolds' Intaglio and C-S-R life-form strategies proposed by Smayda & Reynolds.

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The St. Lucie Estuary, located on the southeast coast of Florida, provides an example of a subtropical ecosystem where seasonal changes in temperature are modest, but summer storms alter rainfall regimes and external inputs to the estuary from the watershed and Atlantic Ocean. The focus of this study was the response of the phytoplankton community to spatial and temporal shifts in salinity, nutrient concentration, watershed discharges, and water residence times, within the context of temporal patterns in rainfall. From a temporal perspective, both drought and flood conditions negatively impacted phytoplankton biomass potential. Prolonged drought periods were associated with reduced nutrient loads and phytoplankton inputs from the watershed and increased influence of water exchange with the Atlantic Ocean, all of which restrict biomass potential. Conversely, under flood conditions, nutrient loads were elevated, but high freshwater flushing rates in the estuary diminished water residence times and increase salinity variation, thereby restricting the buildup of phytoplankton biomass. An exception to the latter pattern was a large incursion of a cyanobacteria bloom from Lake Okeechobee via the St. Lucie Canal observed in the summer of 2005. From a spatial perspective, regional differences in water residence times, sources of watershed inputs, and the proximity to the Atlantic Ocean influenced the composition and biomass of the phytoplankton community. Long water residence times in the North Fork region of the St. Lucie Estuary provided an environment conducive to the development of blooms of autochthonous origin. Conversely, shorter residence times in the mid-estuary limit autochthonous increases in biomass, but allochthonous sources of biomass can result in bloom concentrations of phytoplankton.