The vast diversity of marine phytoplankton, shaped by intricate water dynamics, remains poorly understood in the oligotrophic ocean. In situ studies reveal fine-scale dynamics affecting phytoplankton distribution, leading to abrupt shifts in abundance and biomass referred here as ‘‘phytoplankton community transitions’’ (PCTs). Using a simple nutrient–phytoplankton–zooplankton (NPZ) numerical model, our study proposes a theoretical framework to explain PCTs observed during an oceanographic cruise in the Mediterranean Sea. We consider both a homogeneous and a variable environment, respectively corresponding to the waters on both sides of a front and to the frontal area itself. In the model, PCTs between one community of smaller phytoplankton and one community of bigger phytoplankton are controlled by nutrient supply, but not directly: nutrient supply affects all compartments of the model and creates PCTs by combining bottom-up and top-down controls. This mechanism is observed for both constant (i.e., within a water mass) and pulsed (i.e., in the front) nutrient supply. These results are consistent with in situ observations of biomass proportion across a front. This theoretical framework helps to better understand and plan in situ observations in oceanic regions characterized by fine-scale dynamics and oligotrophic conditions.