To assess the importance of biological factors in determining optical variability, phytoplankton abundance and photosynthetic properties were measured in New England shelf waters as part of the Coastal Mixing and Optics Experiment. Flow cytometric analysis of samples from throughout the water column (about 3 profiles per day) and photosynthesis-irradiance incubations for samples from the euphotic zone (a profile every 1-3 days) were carried out during 3-week cruises in late summer 1996 and spring 1997. Major differences in the phytoplankton community between the two sampling periods were associated with seasonal differences in water temperature and vertical stratification. Prior to Hurricane Edouard, late summer was characterized by a numerically-dominant picophytoplankton assemblage and subsurface maxima near the pycnocline in chlorophyll concentration, light-saturated and light-limited rates of photosynthesis. During spring, picoplankton abundances were very low and biomass and photosynthesis were highest in the top 20 m, especially in early May when a modest phytoplankton bloom was observed. Light-saturated chlorophyll- specific rates of photosynthesis were generally higher in the stratified summer period, while maximum photosynthetic quantum yields tended to be higher in spring when vertical stratification was weaker and nutrient concentrations were higher. Combined with observations of variability in inherent and apparent optical properties of the water column, these results suggest a critical role for biological processes (such as phytoplankton growth and physiological acclimation) in regulating optical variability on the shelf.