By altering the nutritional quality of primary producers, nutrient availability indirectly influences herbivores' population dynamics. In turn, the resulting relationship between diet, growth, and wastes has consequences for nutrient cycling at the ecosystem level. We studied the link between dinoflagellates nutritional requirements and feeding behavior, and its influence on nutrient cycling. We show that long-term shifts in dissolved PO4 concentration in the North Sea are closely linked to biomass trends of heterotrophic dinoflagellates and support this observation with experimental data indicating particularly high phosphorus requirements in dinoflagellates. At the seasonal scale, we observe a negative correlation between natural dinoflagellate abundances and the concentration of dissolved P, and we estimate that, in spring, up to 30% of dissolved P can end up in microzooplankton biomass. Our study highlights that accounting for organismal metabolic requirement provides significant insight in interpreting and predicting nutrient cycles at the ecosystem level.