Hyporheic zones are important in the biogeochemical aspects of stream ecosystems. Groundwater modeling can be used to quantify the influence of geomorphic features and head gradients which are relevant parts of the exchange process. Two and three-dimensional models were built with MODFLOW to evaluate stream-subsurface exchange. The heterogeneity of aquifers was created with Turning Bands and horizontally stratified anisotropic random fields were generated. Aquifer interactions with straight and meandering streams were simulated. Channel morphology is in the investigation since natural streams support healthy aquatic ecosystems due to habitat complexity. Both models consist of a 180x256x30 (x, y, z) grid. The 2-D model is 1 m deep and the 3-D model has 16 layers representing the same depth. The river is simulated by constant-head cells. As the degree of heterogeneity increases so does the volume of water interchanged. Flow variance increases as the lnK variance increases. It decreases for meandering streams when compared to straight-rivers. At transverse cross-sections it is reduced for a given heterogeneity pattern. MODPATH was also used and particle tracking performed to determine a hyporheic exchange residence time distribution. Results show that both aspects of the process interact to control water fluxes across the channel boundaries and subsurface flow paths.