Human development of coastal watersheds has greatly increased nutrient loading and accelerated estuarine and coastal eutrophication. These waters are also affected by climatic perturbations (e.g., droughts, hurricanes, floods), which may be increasing. The ecological effects of these stressors are often most evident at the microbial level, where the bulk of primary production and biogeochemical cycling occurs. Phytoplankton dominate coastal primary production and thus may be indicative of eutrophication and other major perturbations underlying coastal ecosystem change. Using photopigments that are diagnostic for phytoplankton functional groups (chlorophytes, cryptophytes, cyanobacteria, diatoms, and dinoflagellates), we examined the relative responses of these taxonomic groups to nutrient and hydrologic alterations and evaluated their use as indicators of ecological change in the Neuse River Estuary, North Carolina, and Galveston Bay, Texas. Photopigment indicators can be routinely incorporated in water-quality monitoring programs to assess environmental controls on ecosystem structure and function over varying spatial and temporal scales.