The recent increasing of atmospheric turbulence has had considerable impact on the oceanic environment and ecosystems of the Arctic. To understand its effect on phytoplankton community structure, a Eulerian fixed-point observation (FPO) was conducted on the Chukchi shelf in fall 2013. Temporal and vertical distributions of the phytoplankton community were inferred from algal pigment signatures. A strong wind event (SWE) occurred during the observation term, and significant convection supplied nutrients from the bottom layer to the surface. Before the SWE, pigment composition in the warmer, less saline, and nutrient-poor surface waters was diverse with low concentration of chlorophyll-a (chla). Vertical mixing induced by the SWE weakened the stratification and brought sufficient nutrients to enhance diatom-derived pigment concentrations (e.g., fucoxanthin and chlc3), suggesting increases in diatoms. We also developed a model to predict the distribution of major phytoplankton pigment/chla ratios using a profiling multi-wavelength fluorometer (Multi-Exciter) with higher spatio-temporal resolution. The Multi-Exciter also captured changes in pigment composition with environmental changes at the FPO site and at four observation sites 16 km from the location of the FPO. Furthermore, we investigated the change in grazing rates of the major Arctic copepod Calanus glacialis copepodid stage five to assess the interaction between primary and secondary producers during the fall bloom. Increased diatom biomass caused a significant increase in the grazing rate on microphytoplankton (> 20 µm) and a decrease on nanophytoplankton (2-20 µm), indicative of a strong cascade effect because of the reduction of microzooplankton due to the grazing from C. glacialis. We conclude that SWEs during fall might affect food webs via the alternation of seasonal succession of phytoplankton community structure.