The two main parts of the water cycle, groundwater and surface water, could interact together, and the estimation of accurate interaction is now facing many challenges considering man-made activities such as over-pumping. In the present study, a numerical method using a high-resolution digital elevation model (DEM) is employed to understand how groundwater withdrawal effects can change the behavior of groundwater and river interaction in a heterogeneous groundwater system in Stoney Creek Watershed, British Columbia, Canada. The interaction between Groundwater and Stoney Creek (SC) is modeled using three-dimensional MODFLOW-USG. The model parameters including hydraulic conductivity, recharge rate, and aquifer anisotropy are calibrated using PEST, as a parameter estimation code. The calibration of the model is performed using water level data measured in the aquifer and creek in six stations considering the left and right banks of SC from 2015 to 2017. The results show that groundwater is an important source of streamflow in SC. The groundwater contribution to streamflow (Dg) ranges are estimated from 0.01 to 23.6 million cubic meters per year considering river morphology along SC. Under the cumulative groundwater withdrawal scenario, the Dg decreased by 3% in December 2018 compared to the continued current condition scenario in the same month. However, it decreased by 9% in the steady-state conditions. The results of this study and the provided spatial interaction mapping along the SC could help decision-makers better manage water resource issues in the watershed.