This paper describes the results of 10 years of water quality monitoring in the Indian River Lagoon Florida, with special emphasis on the relationships between trends in climatic conditions and the distribution, composition, and abundance of the phytoplankton community. The Indian River Lagoon, which spans 220 km of Florida's east coast, is a region of particular concern because of the rapid rate of human development throughout the region and the hydrologically restricted character of the lagoon, which heightens the potential for algal bloom. Water sampling was carried out on a monthly to twice-monthly basis at six sites located in the northern and central lagoon. The 10-year study included both extended periods of below and above average rainfall. A number of ecologically distinct regions exist within the lagoon, which differ considerably in water exchange properties and watershed inputs. The northern lagoon is characterized by longer water residence times, lower phosphorus concentrations, higher nitrogen concentrations, and more stable salinity conditions than the central lagoon. Mean phytoplankton biovolumes were substantially higher at the sites in the northern lagoon than at the sites in the central lagoon, and algal blooms were more common and intense in the former region. Inter-annual patterns of phytoplankton biovolume were also different in the northern and central lagoon. In the northern lagoon, phytoplankton biovolumes were lowest during the drought period, from the autumn of 1998 to the spring of 2001. By contrast, algal bloom events in the central lagoon were not only less frequent but were not tied to periods of high rainfall. The most widespread and common bloom formers were the potentially toxic dinoflagellate Pyrodinium bahamense var. bahamense and two centric diatoms, Dactyliosolen fragilissimus and Cerataulina pelagica. Many of the biovolume peaks observed over the study period were attributable to these three species. The results of time series modeling of phytoplankton dynamics further highlighted the disparities between the two regions of the lagoon in terms of the suite of parameters that best predict the observed trends in the biomass of phytoplankton. Overall, the outcome of this initial modeling effort in the Indian River Lagoon suggests that time series approaches can help define the factors that influence phytoplankton dynamics.