The influence of pH and substrate concentration on the mixotrophic growth of five microalgae species in presence of acetate or butyrate was evaluated. Acutodesmus obliquus, Auxenochlorella protothecoïdes, two strains of Chlamydomonas reinhardtii, and Chlorella sorokiniana were cultivated at pH from 5 to 10. Acetate was efficiently assimilated by all strains while butyrate uptake was greatly strain dependent. Growth rates at pH values above 8 were reduced while values below 5 or 6 inhibited growth on acetate and butyrate respectively. The influence of acetic and butyric acid concentration was tested. It was demonstrated that the main factor affecting microalgae growth is the concentration of undissociated acid, which can be controlled by pH adjustment. The strains exhibited inhibition threshold concentrations of 71–207 mg·L−1 for acetic acid and of 13–25 mg·L−1 for butyric acid. These findings are crucial for proper control of processes coupling bacterial fermentation and microalgae cultures.