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This paper presents the comparative techno-economic analysis on three different renewable energy sources (i.e. Solar (Thermal and PV) and Wind Energies (WE)) paired with two desalination systems (i.e. Multistage Flash (MSF), Multiple-effect Distillation (MED) and Reverse Osmosis (RO)). The aim of this investigation is to provide thorough technology and economic analysis on the renewable-energy-driven desalination system for Nusa Tenggara Timur (NTT) province. NTT has nationally most districts (20 regions) accounted for water drought every year due to low water precipitation and lack of fresh water resource. It is investigated numerically using Engineering Equation Solver (EES) taking account for most major input considerations. The Solar thermal driven desalination is used to power MSF and MED. The Solar PV and WE are utilized separately for the source of energy for RO system. The results can be utilized as major consideration on which technology should be applied to tackle the fresh water supply drought in NTT. In addition, the economic analysis provides ample explanation for the economic feasibility on the project to be applied. Based on the investigation, the Solar Thermal powered MED and MSF promises biggest feasibility techno-economically with lowest LCOEs.