To fully understand the economic viability and implementation strategy of the emerging algae-based de- salination technology, this study investigates the economic aspects of algae-based desalination system by comparing the life-cycle costs of three different scenarios: (1) a multi-stage microalgae based desalina- tion system; (2) a hybrid desalination system based on the combination of microalgae and low pressure reverse osmosis (LPRO) system; and (3) a seawater reverse osmosis (SWRO) desalination system. It is identified that the capital expenditure (CAPEX) and operational expenditure (OPEX) of scenario 1 are significantly higher than those of scenarios 2 and 3, when algal biomass reuse is not taken into consider- ation. If the revenues obtained from the algal biomass reuse are taken into account, the OPEX of scenario 1 will decrease significantly, and scenarios 2 and 3 will have the highest and lowest OPEX, respectively. However, due to the high CAPEX of scenario 1, the total expenditure (TOTEX) of scenario 1 is still 27% and 33% higher than those of scenarios 2 and 3, respectively. A sensitivity study is undertaken to understand the effects of six key parameters on water total cost for different scenarios. It is suggested that the elec- tricity unit price plays the most important role in determining the water total cost for different scenarios. An uncertainty analysis is also conducted to investigate the effects and limitations of the key assumptions made in this study. It is suggested that the assumption of total dissolved solids (TDS) removal efficiency of microalgae results in a high uncertainty of life-cycle cost analysis (LCCA). Additionally, it is estimated that 1.58 megaton and 0.30 megaton CO2 can be captured by the algae-based desalination process for scenarios 1 and 2, respectively, over 20 years service period, which could result in approximately AU $18 million and AU $3 million indirect financial benefits for scenarios 1 and 2, respectively. When algal biomass reuse, CO2 bio-fixation and land availability are all taken into account, scenario 2 with hybrid desalination system is considered as the most economical and environmentally friendly option.