Global demand for water is rising. A sustainable and energy efficient approach is needed to desalinate brackish sources for agricultural and municipal water use. Genetic variation among two algae species, Scenedesmus species (S. sp.) and Chiorella vulgaris (C. vulgaris), in their tolerance and uptake of salt (NaCl) was examined for potential bio-desalination of brackish water. Salt-tolerant hyper-accumulators were evaluated in a batch photobioreactors over salinity concentration ranging from 2 g/L to 20 g/L and different nutrient composition for their growth rate and salt-uptake. During algae growth phase, the doubling time varied between 0.63 and 1.81 days for S. sp. and 3.1 to 5.9 for C. vulgaris. The initial salt-uptake followed pseudo first order kinetics where the rate constant ranged between -3.58 and -7.68 day(-1) reaching up to 30% in a single cycle. The halophyte algae S. sp. and C. vulgaris that were selected for pilot-scale studies here represent a promising new method for desalination of brackish waters. Halophytic technologies combined with the potential use of algae for biofuel, which offsets energy demand, can provide a sustainable solution for clean, affordable water and energy.