The global water shortage alert has been upgraded to a higher risk level. Consequently, a sustainable approach for ecofriendly, energy efficient water desalination is required for agricultural and municipal water reuse. In this study, an energy-efficient biological desalination process was used to treat chloride anions, which are the most abundant anion salt in seawater. Three algal species were studied: Scenedismus arcuatusa (S. arcuatusa), Chlorella vulgaris (C. vulgaris), and Spirulina maxima (Sp. maxima), under different operating conditions (saline concentrations, contact time, high light intensity, and CO2 supply), and two kinetic models were used. It was identified that under a high light intensity and CO2 supply, S. arcuatusa enhanced chloride removal from 32.42 to 48.93%; the daily bioaccumulation capacity (Qe), according to the kinetic models, was enhanced from 124 to 210 mg/g/day; and the net biomass production was enhanced from 0.02 to 0.740 g/L. The EDX analysis proved that salt bioaccumulation may be attributed to the replacement of Ca2+ and Mg2+ with Na+ and K+ through algal cells. The study’s findings provide promising data that can be used in the search for novel energy-efficient alternative ecofriendly desalination technologies based on algae biological systems with biomass byproducts that can be reused in a variety of ways.