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 (Q_e), 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.