The effects of autotrophic and mixotrophic conditions on microalgae growth and nutrient removal efficiency from synthetic wastewater by different microalgae were investigated. Although several studies have demonstrated the suitability of microalgae technologies for ammonia rich wastewater treatment, only a few have been used for treatment of phosphate-rich industrial wastewaters. In this work, six microalgae were cultivated in batch mode in growth medium with a high phosphate concentration (0.74 Mm PO43−-P) and different carbon sources (ammonium acetate and sodium bicarbonate) without CO2 supplementation or pH adjustment. Their potential for nutrient removal and biomass generation was estimated. The biomass growth in the reactors was modeled and the data aligned to the Verhulst model with R2 > 0.93 in all cases. C. pyrenoidosa ACUF_808 showed the highest final biomass productivity of 106.21 and 75.71 mg·L−1·d−1 in medium with inorganic and organic carbon source, respectively. The highest phosphorus removal efficiency was 32% with C. vulgaris ACUF_809, while the nitrate removal efficiency in all reactors exceeded 93%. The coupled cultivation of the novel isolated strains of C. pyrenoidosa and C. vulgaris under mixotrophic conditions supplemented with ammonium acetate might be a promising solution for simultaneous nitrate and phosphate removal from phosphorus-rich wastewaters.