The rapid rate of development in the South Carolina (SC) coastal zone has heightened public concern for the condition of the state's estuaries, and alerted scientists to the potential that novel and adverse effects on estuarine ecosystems may result. Although well-developed databases from long-term monitoring programs exist for many variables valuable in predicting and following system responses, information on phytoplankton distributions in SC estuaries has lagged. Knowledge of the dynamical relationship between environmental (e.g., nutrient quantity and quality) and biological (e.g., grazing) regulation, and phytoplankton biomass and composition is critical to understanding estuarine susceptibility to eutrophication or harmful algal blooms (HABs). Recently, SC scientists from federal, state, and academic institutions established a collaborative monitoring program to assess HAB distribution and ecology statewide. The South Carolina Harmful Algal Bloom Program includes: a) intensive temporal monitoring at areas of known HAB occurrence or those exhibiting symptoms potentially related to HABs (e.g., prevalent fish lesions), b) extensive spatial monitoring in coordination with existing statewide efforts, c) a citizen volunteer monitoring network, d) nutrient response bioassays, and e) laboratory-based physiological experiments on HAB isolates. By combining "trip-wire" surveillance and rapid response systems, routine monitoring of environmental parameters and HAB distribution, and process-oriented studies examining the physiological functioning of HAB species, an enhanced understanding of the impact and environmental control of HABs in SC estuaries will be achieved. The application of this approach to studies on the distribution and physiological ecology of a new widespread SC red tide, and to the discovery of several potentially toxic blooms (including Pfiesteria) in SC holding ponds, are described.