The paper deals with the possibility of using flue gas as a nutrient source for microalgae cultivation in a bubble column photobioreactor. The experiments performed on a vertical tubular photobioreactor determined the concentrations of the flue gas species that pass from the flue gas into the cultivation medium. The flue gas used for experiments was a gas mixture of different pollutants, e.g. SOx, NOx, or CO2, with a composition typical for waste-to-energy facilities. The paper is supplementary to the laboratory experiments. The objective of the multiphase CFD analysis is to develop the numerical model for mass transfer predictions in photobioreactors. The model employs the Henry’s law for interphase equilibrium and the penetration model for the mass transfer coefficient.