The high variability in physical, biological, and chemical properties in coastal waters have limited our ability to sample the appropriate timescale and space scale to resolve physical forcing of the ecosystem. To improve our understanding, a multiplatform adaptive sampling program at the Long-term Ecosystem Observatory (LEO-15) off the coast of New Jersey examined the relationship between episodic summertime upwelling and downwelling events and the corresponding dynamics in bulk phytoplankton biomass and community structure. Inherent and apparent optical properties were concurrently measured to evaluate the use of optics to improve future sampling coverage in coastal regions. Results indicate peak chlorophyll biomass tracked the maximum density gradient and that increasing surface phytoplankton biomass was associated with decreasing stratification offshore over time. Diatoms dominated the study site; however, significant shifts in cyanobacteria and dinoflagellate communities were observed. Dinoflagellate and cyanobacteria communities responded inversely to episodic events, with cyanobacteria being favored during intense downwelling. Differences in phytoplankton absorption properties significantly changed the corresponding in water inherent optical properties, allowing for characterization of the community structure from measurements of above water hyperspectral reflectance.