Visual MODFLOW, a three dimensional groundwater flow model, was used to analyze effects of a weir construction in an alluvial stream on the nearby groundwater flow system. A hypothetical conceptual model was developed to investigate how the groundwater level and the water budget could change after a weir construction depending on the location of tributary streams. A site example, dealing with the Juksan weir installed in the Yeongsan River, was also demonstrated to predict the effects of the weir construction. Model results show that impacts of a weir construction on the groundwater flow system greatly vary depending on how far a tributary is located and whether it is located downstream or upstream from the weir. Therefore, consideration of the location of tributaries in planning the location of a weir could effectively minimize the impacts of a weir construction on the groundwater flow system. It is also demonstrated that model results are highly dependent upon how the model is dealing with small tributaries and agricultural drainage channels, which can be easily found nearby the main streams, acting as major water bodies for groundwater discharge. The model for the Juksan area shows that the weir construction will change the direction of groundwater flow in some areas, leading to changes of groundwater quality and interaction of the Yeongsan River to the aquifer from a gaining to a losing stream. The model also predicted the areas where rise of groundwater level caused by the Juksan weir could adversely affect plant growth, and thereby suggested installing new drainage channels as a countermeasure to drawdown the groundwater level.