Microalgal metabolism is affected by the surrounding environment and nutrients such as phosphorus (P) and nitrogen (N) are essential for optimal metabolism, as well as trace amounts of essential metals such as zinc (Zn); although in higher doses than required, Zn can be toxic. Lead (Pb) is a non-essential metal that can harm organisms from different trophic levels. In the environment, algae are exposed to several stressors simultaneously and adapt their metabolism. In the present study, we evaluated P limitation combined with environmental concentrations of Zn or Pb to the freshwater microalga Raphidocelis subcapitata regarding growth, pigments production, and photosynthetic parameters. Our results indicate that P limitation affected the growth, pigments production, relative maximum electron transport rate (rETRmax), and saturation irradiance; while Pb altered growth, pigments production, and maximum quantum yield; and Zn affected pigment production, photochemical and non-photochemical quenching, and rETRmax. However, the combination of metal and P limitation resulted in synergistic responses, i.e., higher damages than the isolated stressors, in growth, maximum and effective quantum yield, and in the rapid light curve parameters. On the other hand, antagonism, i.e., lower damages than isolated stressors, was observed in pigments production and non-photochemical quenching, suggesting that algae activated defense mechanisms to cope with both stressors simultaneously. In addition, our results indicate an algal metabolism adjustment to P limitation and highlight the importance of considering physicochemical water characteristics when defining regulations of acceptable levels of metals in aquatic ecosystems.