The demand for water in the Stoney Creek watershed, British Columbia, necessitates the management of groundwater and surface water as hydraulically connected systems. However, the interactions between groundwater and surface water in this watershed have not been investigated yet. This was addressed by developing a new numerical groundwater model for the watershed that incorporates surface water features. A particularity of the model is that it was bounded by two surface water features (Stoney Creek and the Nechako River/Tachick Lake system). A surface and groundwater level monitoring program was also implemented to independently test the predictions from the model. The simulated regional water table indicated that Tachick Lake is a groundwater flow-through system, with discharging groundwater either exported by surface outflow or groundwater recharge, whereas Stoney Creek was regionally gaining and largely groundwater-fed. The comparison between simulated and observed heads showed that the numerical groundwater model is capable of estimating the location of the water table across the watershed with a reasonable precision (correlation coefficient of 89%) and provides a platform to evaluate potential variations in the groundwater flow system under different climate change and development scenarios. Results of this study could be helpful for decision makers in allocating the groundwater and developing sustainable water resources strategies in the Stoney Creek Watershed.