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Sustainable management of groundwater resources is essential for sound groundwater development, especially in sensitive salt-affected areas. In Northeast Thailand, the Central Huai Luang Basin, underlain by rock salt, is the source of groundwater and soil salinity. The future sustainable groundwater development yield was assessed under the plausible uncertainty of hydrogeological and projected climate scenarios that could impact the groundwater system. The SEAWAT and HELP3 models were used to simulate groundwater system. The four alternative scenarios of hydrogeological conceptual models were formulated to determine the impact on groundwater system and sustainable groundwater yield. In addition, impacts of projected climate conditions on each alternative model were explored. The results indicate that variable depths and thicknesses of rock salt layers have a higher impact on groundwater salinity distribution and sustainable yield estimations than model boundary conditions. Groundwater salinity, shallow water table areas, and sustainable yield projections vary substantially depending on the possible conceptual model scenarios. It is clear that the variable hydrogeological models affect groundwater sustainable yields.