The use of MODFLOW and related models to simulate hyporheic exchange in near-stream environments has become increasingly popular. These models are of interest because they have the power to simulate head gradients that drive exchange between streams and alluvial aquifers. This application of relatively well-known groundwater flow models is not without new challenges in model design and implementation. Here we discuss 3 specific limitations in hyporheic groundwater flow modeling: uncertain hydraulic conductivity fields, uncertain characterization head fields represented by the water surface of the stream, and poorly defined boundary conditions. We compare results of models developed for steep mountain streams and lower gradient arctic streams. These examples suggest that there is a definite need to develop new field techniques to better characterize streambed sediments, stream water velocity distributions, and sub-stream depth to bedrock (or other confining layers), in order to develop more accurate groundwater flow models.