The use of microalgae is a new and cost-effective biological method for the desalination of saline and brackish waters. For this purpose, after sampling and preparing BG-11 medium with deep aquifer well water, some physicochemical parameters of water were measured and the possibility of reducing the salinity of deep aquifer well water by Scenedesmus obliquus and Chlorella vulgaris algae with cell densities of 1.25 and 2.5×10⁶ cells/mL was investigated. The results showed that the highest salinity, total dissolved solids value (TDS), Na⁺, Hardness, Nitrate, Phosphate removal and the highest biological desalination rate were observed in S. obliquus algae with a density of 2.5×10⁶, respectively with 9.6%, 27.14%, 7.34%, 25%, 67.01 %, 97.32% reduction, and 28.5±2.50 % for biological desalination rate which showed a significant difference compared to C. vulgaris algae. The highest Chloride removal was observed in C. vulgaris with a density of 2.5×10⁶ cells/mL from 2840 to 828.33±108.45 mg/L (70.83% reduction). The results of dry biomass and algal cell numbers indicated that the highest values were assigned to low and high densities of C. vulgaris algae, with values of 1.03±0.08 and 0.99±0.04 g/L, and 46.35±4.45 and 43.53±4.86 (×10⁶cells/mL), respectively. According to the results, both algae have the ability to reduce deep aquifer well water salinity. Therefore, considering the impact of higher algae densities on further desalination, it is recommended that higher densities be tested.