In order to include lateral flow, a coupled land-surface groundwater model is used in this investigation to provide improved initial surface conditions for atmospheric simulations of flow over Owens Valley in California, a region with mountainous topography. The coupled model consists of a variably-saturated groundwater model coupled to a land-surface model driven by meteorological forcing during a multi-year spin-up procedure. Use of such a physically-based coupled model allows for realistic representation of surface and deep soil moisture distributions that reflect topographically-influenced variations in the valley region, without requiring calibration to the particular catchment or relying on observational data. In previous work, we simulated a 2D slice of Owens Valley using this coupled model, and used the results to prescribe altitude-dependent soil moisture for initialization of atmospheric simulations. In the current work, extension to 3D simulations allows for surface-subsurface flows in all directions within the domain. Results from the 3D coupled model are compared to results from a traditional land-surface model and surface observations from T-REX.