Algal treatment methods have been widely used in nutrient removal studies. However, in most cases, the experimental conditions have not been fully complied with actual conditions. For instance, the effect of algae acclimation to wastewater medium on cell growth and removal efficiency has generally been ignored in laboratory scale experiments. This paper investigates the effect of acclimation on cell growth and nutrient uptake rates of Arthrospira platensis and Chlorella vulgaris. For this purpose, batch reactors, which contained the synthetic secondary effluent, had been inoculated by acclimated algae cells and the growth parameters were measured daily, as well as nutrient concentration. A significant decrease (P < 0.05) in chlorophyll-a content of acclimated A. platensis was observed, although there was no significant change in specific growth rate (mu) and doubling time (dt), in comparison with the non-acclimated ones. Moreover, the acclimation process changed the chlorophyll-a content and kinetic parameters of Chlorella vulgaris. Furthermore, t test results showed a significant increase in removal rate of nitrogen compounds through the acclimation. Residence time of A. platensis and C. vulgaris was also reduced through the acclimation by approximately 50% and 25%, respectively.