Demographic growth in developing countries has increased domestic wastewater generation, posing environmental and health risks due to nitrogen and phosphorus accumulation, the main contributors to eutrophication. This study explores microalgae–bacteria consortia for nutrient removal, using Chlorella sp. for its high pollutant assimilation efficiency and biomass production. A lab-scale experiment was designed using response surface methodology to optimize key variables, revealing that lighting and the culture medium significantly influenced biomass production and nutrient removal, with lighting having the strongest statistical impact (p = 0.0002). The optimal conditions (18 μmolm⁻² s⁻¹ light, municipal wastewater) achieved nitrogen and phosphorus removal efficiencies of 87.16% and 94.43%, respectively. A mathematical model was developed with two independent systems: (1) the first describes biomass generation via photosynthesis, considering CO₂ as a limiting substrate, while (2) the second models nitrogen and phosphorus consumption, assuming nitrogen as limiting substrate and introducing an intermediate (I) that couples phosphorus and nitrogen removal. This coupling is regulated by factor k, which represents a percentage of the total consortium consumption rate. Model predictions showed high accuracy for biomass (SE = 0.07186) and phosphorus (SE = 0.63065), but nitrogen exhibited greater deviation (SE = 3.40285). These findings highlight the system’s potential as a sustainable and cost-effective wastewater treatment alternative.