© 2015, Coastal and Estuarine Research Federation. Prince William Sound supports many commercially and culturally important species. The phytoplankton community dynamics which support and sustain the high biomass and diversity of this ecosystem are largely unknown. The aim of this study was to describe the phytoplankton community composition during the summer, the time at which this system supports many additional migrants and commercially important fisheries. Phytoplankton community composition (pigments), dissolved nutrients, Secchi depth, total and particulate organic carbon and nitrogen, and export to deep water were measured during the summers of 2008–2010. In addition, natural abundance stable isotopes (δ13C and δ15N) of particulate organic matter (POM) and faunal samples were measured in 2010. The analysis of the phytoplankton community composition using multivariate statistics showed that changes over the summer were driven by changes in the proportion of the dominant groups: diatoms, dinoflagellates, cyanobacteria, cryptophytes, chlorophytes, and prasinophytes. These changes were driven by changes in nutrients including an organic nitrogen source, phosphate, and silica and correspond to shifts in particulate concentrations. A consistent pattern was observed each year: a large Noctiluca sp. bloom in June concurrent with low nutrients, low diversity, and high particulate organic carbon (POC) concentrations was followed by a shift in the phytoplankton community to a more diverse smaller size class community in July and equilibrating in August. This annual summer bloom could be an important contributor to the energy and nutrient inputs at the base of the regional marine food web.