The phytoplankton community size structure is a significant factor in the ecological and biogeochemical functioning of marine ecosystems. Various environmental factors, including nutrients, can cause variations in the size structure of phytoplankton community, ultimately determining the potential for downward carbon transport and productivity in marine ecosystems. In the present study, microscale spatial variation in phytoplankton size structure was investigated at two coastal stations having different nutrient environments. The variation in phytoplankton size structure was characterized by a significantly (p < 0.05) higher contribution of larger cells and diminishing abundance of picoplankton under increasing nutrient concentrations observed at both sites, although at different threshold unfractionated phytoplankton chlorophyll a biomass levels. The average percent contributions of picoplankton to total biomass were 30.02 and 19.07% at less enriched site I and at enriched site II, respectively. Thus, we concluded that the variation in phytoplankton size structure was led by the factors that regulated the contribution of large phytoplankton cells; that is, the dominance of picoplankton was only possible when nutrient concentrations precluded accumulation of the larger size classes in the phytoplankton community.