Phytoplankton community pigment composition and water quality were measured seasonally along salinity gradients in two minimally urbanized salt marsh estuaries in South Carolina in order to examine their spatial and temporal distributions. The North Inlet estuary has a relatively small watershed with minimal fresh water input, while the Ashepoo, Combahee, and Edisto (ACE) Basin is characterized by a relatively greater influence of riverine drainage. Sampling stations were located in regions of the estuaries experiencing frequent diurnal tidal mixing and had similar salinity and temperature regimens. Phytoplankton community pigment composition was assessed by using high-performance liquid chromatography (HPLC) and multivariate statistical analyses. Shannon diversity index, principal-component, and cluster analyses revealed that phytoplankton community pigments in both estuaries were seasonally variable, with similar diversities but different compositions. The temporal pigment patterns indicated that there was a relatively weak correlation between the pigments in ACE Basin and the relative persistence of photopigment groups in North Inlet. The differences were presumably a consequence of the unpredictability and relatively greater influence of river discharge in the ACE Basin, in contrast to the greater environmental predictability of the more tidally influenced North Inlet. Furthermore, the timing, magnitude, and pigment composition of the annual phytoplankton bloom were different in the two estuaries. The bloom properties in North Inlet reflected the predominance of autochthonous ecological control (e.g., regenerated nutrients, grazing), and those in ACE Basin suggested that there was greater influence of allochthonous environmental factors (e.g., nutrient loading, changes in turbidity). These interestuarine differences in phytoplankton community structure and control provide insight into the organization of phytoplankton in estuaries.Processes and mechanisms that determine the spatial and temporal patterns of phytoplankton have been a central focus of marine research for decades. This research has led to the identification of biotic and abiotic factors that regulate primary productivity and the development of models that describe phytoplankton growth dynamics under specific environmental conditions (4). Phytoplankton communities are multispecies communities which are highly complex in terms of their diversity and dynamics. Successional shifts in phytoplankton community structure are primarily due to changes in environmental variables (e.g., degree or type of nutrient limitation) and/or shifts in higher trophic levels (e.g., micro-versus mesozooplankton) (23,35,40,54,56). How phytoplankton community composition changes with environmental variables and/or preferential grazing by herbivores is not well understood, particularly in estuarine ecosystems. Identifying the ecological variables that regulate phytoplankton community structure is essential for facilitating the development of broad hypotheses underlying our...