The aim of this article is the comparison of input options of river boundary condition of MODFLOW - three-dimensional numerical simulation model of groundwater flow. The water level in stream flowing through territory of hydrogeological layer can be computed via three built-in modules: River, Stream and Streamflow-Routing. In this study the code MODFLOW is used to simulate idealized aquifer and stream. The differences between computed groundwater table showed to be minimal, thus in case of modules Stream and Streamflow- Routing they are equally usable as using module River with external one or two-dimensional simulation of surface water flow, which is more time-consuming process. However, this applies only to idealized, simplified conditions of the modeled environment. For more complex simulation of flow in streams with irregular structure of the streambed is necessary to use either an external simulation or use the Streamflow-Routing module, which includes the possibility to enter more complex hydraulic flow parameters in the model.