The York River possesses a diverse phytoplankton community represented by a variety of algal species that includes both freshwater and estuarine flora. The mean annual monthly range of abundance is ca. 5–20 X 106 cells L−1 with an extended bi-modal pattern that begins with an early spring diatom peak (March) that declines into early summer. The development of a more diverse representation of taxa in the summer results in a secondary late summer-early fall peak. Diatoms are the dominant phytoplankton component throughout the entire estuary including a variety of pennate and centric species such as Asterionella formosa and Aulacoseira granulata. Dinoflagellates are more common and abundant in the lower segments of the York River where they have been associated with re-occurring and extensive “red tide” blooms. These include Cochlodinium polykrikoides, Heterocapsa triquetra, Heterocapsa rotundata, Scrippsiella trochoidea, and Prorocentrum minimum. Cynobacteria, commonly referred to as blue-green algae, include unicellular, colonial, and filamentous taxa that are predominantly freshwater species. Among the more common taxa are Microcystis aeruginosa, a potential bloom producer, Merismopedia tenuissima, Oscillatoria spp., Dactylococcopsis spp., Chroococcus spp. and Synechococcus spp. The cyanobacteria are generally considered a nuisance category that do not represent a favorable food resource, and are commonly associated with increased trophic status. Chlorophytes or green algae, including Ankistrodesmus falcatus, Chlorella spp., Pediastrum duplex, Scenedesmus acuminatus and Scenedesmus dimorphus are more common from spring to fall with lowest abundance in winter. Overall, the phytoplankton status in the York has been classified as poor/fair condition. Further studies are needed regarding interrelationships between the floral and faunal components of the plankton community and linkages to water quality and physical environmental factors in the system. In addition, continued observations regarding long-term trends in phytoplankton abundance and composition need to be followed with emphasis on any increasing presence of potentially harmful phytoplankton species.