The Saemangeum Reservoir is located on the western coast of the Republic of Korea and is embanked by a 33.9 km sea dike. The Saemangeum River Basin consists of the Mankyeong and Dongjin river basins, which have an immediate influence on the hydrodynamic characteristics of the Saemangeum Reservoir. The objectives of this study are to simulate a series of temporal and spatial distributions of water temperature and salinity to estimate the required time for desalination of the Saemangeum Reservoir and to suggest possible timing for the first agricultural water supply. To achieve this objective, a hydrodynamic numerical model is calibrated and five conditions are considered for estimating the required desalination period. The simulated period for desalination is 2.0 ‐ 2.5 years considering the conditions of percolated seawater and leached salt from the reclaimed areas, while the period of desalination is expected to take more than five years considering the conditions of salt elution from the benthic layer. Under the conditions that rural water can mostly be supplied from the surface layer of the Saemangeum Reservoir, it is expected to supply water for agricultural use in three years after the desalination of the surface layer of the reservoir. Copyright © 2016 John Wiley & Sons, Ltd.