This study analyzes the impacts of agricultural water shortages in Korea using a combined top-down and bottom-up model. A multi-region multi-output agricultural sector model with detailed descriptions of production technologies and water and land resource constraints has been combined with a standard CGE model. The impacts of four different water shortage scenarios were simulated. It is shown that an active adaptation of crop choices occurs in even the regions with relatively abundant water resources in order to respond to the change in relative output prices caused by water shortages. We found that although the losses in production values are not quite large despite water shortages due to the price feedbacks, the loss in GDP is substantial. We show that our combined approach has advantages in deriving region and product specific production effects as well as the overall GDP loss effect of water shortages.