This study investigates the role of the water-energy-nexus in transition plans to achieve a future system with a higher share of renewable energy and lower excess water extraction. Applying a novel nexus approach, an interactive multi-period model is proposed to study the synergies of sustainable water and energy supply planning, taking into account operational flexibility of the water sector and its compatibility with inherent intermittency of variable renewable resources. For investigating synergies in designing both energy systems and water systems together, the path of technology cost reduction is assumed to be a function of experience and knowledge and estimated using two-factor learning curves. The learning-by-searching rate was higher than the learning-by-doing rate for utility-scale wind, photovoltaic and reverse osmosis desalination technologies, ensuring research & development investment can play a chief role in the development of these industries. The levelized cost and capacity factor of photovoltaic and wind resources in the Middle East were calculated using data from 81 projects. The results showed that planning the water and energy sectors as endogenous parts of one integrated system brings potential synergies. The levelized cost of variable renewable energy decreased by 20% and the levelized cost of desalinated water dropped 4%.