Accurate representation of groundwater flow and solute transport requires a sound representation of the underlying geometry of aquifers. Faults can have a significant influence on the structure and connectivity of aquifers, which may allow permeable units to connect, and aquifers to seal when juxtaposed against lower permeability units. Robust representation of groundwater flow around faults remains challenging despite the significance of faults for flow and transport. We present a methodology for the inclusion of faults utilizing the unstructured grid features of MODFLOW-USG and MODFLOW 6. The method focuses on the representation of fault geometries using non-neighbor connections between juxtaposed layers. We present an illustration of the method for a synthetic fluvial aquifer. The combined impact of the heterogeneous aquifer and fault offset is clearly visible where channel features at different depths in the aquifer were connected at the fault. These results highlight the importance of representing fault features in groundwater flow models.