Many current biogeochemical models rely on an autotrophic versus heterotrophic food web representation. However, in recent years, an increasing number of studies have begun to challenge this approach. Several authors have highlighted the importance of protists capable of combining photoautotrophic and heterotrophic nutrition in a single cell. These mixotrophic protists are known to play an important role in the carbon cycle. Here, we present a new biogeochemical model that represents the food web using variable stoichiometry. It contains the classic compartments such as zooplankton, phytoplankton, and heterotrophic bacteria and a newly added compartment to represent two types of mixotrophic protists: non-constitutive mixotrophs (NCMs) and constitutive mixotrophs (CMs). We demonstrate that the model correctly reproduces the characteristics of NCMs and CMs and proceed to study the impact of light and nutrient limitation on planktonic ecosystem structure in a highly dynamic Mediterranean coastal area, namely the Bay of Marseille (BoM, France), paying special attention to the dynamics of mixotrophic protists in these limiting conditions. In addition, we investigate the carbon, nitrogen, and phosphorus fluxes associated with mixotrophic protists and showed the following: (i) the portion of the ecosystem in terms of the percentage of carbon biomass occupied by NCMs decreases when resources (nutrient and prey concentrations) decrease, although their mixotrophy allows them to maintain a carbon biomass almost as significant as the copepod one (129.8 and 148.7 mmol C m−3, respectively), as photosynthesis increases as a food source, and (ii) the portion of the ecosystem in terms of the percentage of carbon biomass occupied by CM increases when nutrient concentrations decrease due to their capability to ingest prey to supplement their N and P needs. In addition to providing new insights regarding the conditions that lead to the emergence of mixotrophs in the BoM, this work provides a new tool to perform long-term studies and predictions of mixotroph dynamics in coastal environments under different environmental forcings.